As filed with the Securities and Exchange Commission on September 14, 2004July 18, 2006

Commission File No.: 333-

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM S-3

REGISTRATION STATEMENT

UNDER

THE SECURITIES ACT OF 1933

TRANSGENOMIC, INC.

(Exact Name of Registrant As Specified In Its Charter)

12325 Emmet Street Omaha, Nebraska 68164 (402) 452-5400

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive offices)

Collin J. D’SilvaMichael A. Summers

President and Chief ExecutiveFinancial Officer

12325 Emmet Street Omaha, Nebraska 68164 (402) 452-5400

(Name, address and telephone number of Agent for Service)

Copies to:

Steven P. Amen

Kutak Rock LLP

1650 Farnam Street

Omaha, Nebraska 68102

Tel: (402) 346-6000

Fax: (402) 346-1148

APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC: From time to time after the effective date of this Registration Statement as determined by market conditions.

If the only securities being registered on this Form are being offered pursuant to dividend or interest reinvestment plans, please check the following box.¨

If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, other than securities offered only in connection with dividend or interest reinvestment plans, check the following box.x

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.¨

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.¨

If delivery of the prospectus is expected to be made pursuant to Rule 434, please check the following box.¨

CALCULATION OF REGISTRATION FEE

The prospectus forming a part of this Registration Statement, as such prospectus may be amended or supplemented from time to time (the ”Prospectus”), shall be deemed to relate to the 4,717,099 shares of common stock being registered pursuant to this Registration Statement and, pursuant to Rule 429 the General Rules and Regulations under the Securities Act of 1933, to (i) 3,729,447 shares of common stock registered for resale by selling stockholders pursuant to the registration statement on Form S-3 (Registration No. 333-108319), (ii) 595,918 shares of common stock registered for resale by selling stockholders pursuant to the registration statement on Form S-3 (Registration No. 333-111442) and (iii) 2,557,842 shares of common stock registered for resale by selling stockholders pursuant to the registration statement on Form S-3 (Registration No. 333-114661) (collectively, the “Prior Registration Statements”). As such, this registration statement constitutes Post-Effective Amendment No. 1 to each of the Prior Registration Statements. The amount of filing fees associated with the common stock registered pursuant to the Prior Registration Statements (calculated at the fee in effect at the time of filing of the Prior Registration Statements) is $407.74, $227.68 and $784.05, respectively.

WeRegistrant hereby amendamends this Registration Statement on such date or dates as may be necessary to delay its effective date until we filethe Registrant files a further amendment which specifically states that this Registration Statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until this Registration Statement shall become effective on such date as the Commission, acting according to Section 8(a), may determine.

The information in this prospectus is not complete and may be changed. These securities may not be sold until the registration statement filed with the Securities and Exchange Commission is effective. This prospectus is not an offer to sell these securities and is not seeking an offer to buy these securities in any state where the offer or sale is not permitted.

Subject to Completion, dated September 14, 2004July 18, 2006

PRELIMINARY PROSPECTUS

11,600,30624,090,795 Shares

TRANSGENOMIC, INC.

COMMON STOCK

This Prospectusprospectus covers 11,600,30624,090,795 shares (“Shares”) of our common stock that the selling stockholders listed under “Selling Stockholders” may offer and resellsell from time to time. These Shares consist of:

The selling stockholders may sell the shares at the then prevailing market price for the shares at the time of the sale, or at other prices. The last reported sale price for our common stock on September 13, 2004July 12, 2006 was $1.16$0.45 per share. The selling stockholders are offering the Shares as described under “Plan of Distribution.” We will not receive any of the proceeds from the sale of these shares by these stockholders.

the selling stockholders, but will be entitled to the proceeds from the exercise of outstanding warrants.

Our common stock is listed on the Nasdaq National Market under the symbol “TBIO.”

The selling stockholders are offering the common stock as described under “Plan of Distribution.”

Investing in our common stock involves a high degree of risk. You should carefully consider the information under the heading “Risk Factors”“Risk Factors” beginning on page 57 of this Prospectus before buying shares of our common stock.

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or passed upon the adequacy or accuracy of this prospectus. Any representation to the contrary is a criminal offense.

, 2004

2006

TABLE OF CONTENTS

Forward-Looking Statements

This prospectus contains or incorporates by reference certain forward-looking statements. Many of these forward-looking statements refer to our plans, objectives, expectations and intentions, as well as our future financial results and are subject to risk and uncertainty. You can identify these forward-looking statements by words such as “expects,” “anticipates,” “intends,” “plans,” “may,” “will,” “believes,” “seeks,” “estimates” and similar expressions. Because these forward-looking statements involve risks and uncertainties, there are many factors that could cause our actual results to differ materially from those expressed or implied by these forward-looking statements, including those discussed under “Risk Factors” in this Prospectus or described in reports that we file from time to time with the Securities and Exchange Commission, such as our Forms 10-K and 10-Q.

You should rely only on the information contained in or incorporated by reference into this Prospectus. We have not authorized any other person to provide you with different information. If anyone provides you with different or inconsistent information, you should not rely on it. The information in this Prospectus is current as of its date. Our business, financial condition, results of operations and prospects may have changed since that date.

This Prospectus references the following registered trademarks which are the property of Transgenomic: DNASEP^® Columns, WAVE^® System, WAVEMAKER^® Software, TRANSFORMING THE WORLD^® for Laboratory Equipment, TRANSGENOMIC^® and the Globe Logo^®; MutationDiscovery.com^® Website, OLIGOSEP^® for Systems and Reagents, OPTIMASE^® Polymerase, RNASEP^® Columns, WAVE OPTIMIZED^® reagents, and WAVE^® MD Systems. Additionally, this Prospectus references the following trademarks which are the property of Transgenomic: MitoScreen^™ Kits, ProtocolWriter^™ Software, Navigator^™ Software, THE POWER OF DISCOVERY^™ for Lab Reagents and Educational Programs, and Surveyor^™ Nuclease. All other trademarks or trade names referred to in this Prospectus are the property of their respective owners.

ABOUT THIS PROSPECTUS

This Prospectus does not contain all of the information you need to consider before buying our common stock. Additional important information is contained in the documents that are incorporated by reference into this Prospectus, including more detailed financial statements and the notes thereto. See “Incorporation of Certain Documents By Reference.” As a result, information presented in this Prospectus is qualified in its entirety by this additional information. We urge you to carefully read this entire Prospectus, along with the additional information that is incorporated by reference into this Prospectus, before investing in our common stock. In particular, you should carefully consider the information discussed under “Risk Factors”.Factors.” All references to “we,” “us” or the “Company””Company” in this Prospectus mean Transgenomic, Inc.

TRANSGENOMIC, INC.

Our Business

We develop, assemble, manufacture and market versatile products and provide innovativeanalytical services to the medical research, clinical and pharmaceutical markets for use in genetic variation analysis. Products and services are sold through a direct sales force in the United States and throughout much of Western Europe. For the rest of the world, products and services for the synthesis, purificationare sold through more than 25 dealers and analysis of nucleic acids. Our operations fall into two principal business units, BioSystemsdistributors located in those local markets. Net sales are categorized as bioinstruments, bioconsumables and Nucleic Acids. Our BioSystems products include our WAVE^® automated instrument systems, WAVE associated consumable products and other related consumable products. Our Nucleic Acidsdiscovery services.

Until recently, we also operated a segment that developed, manufactured and marketed chemical building blocks for nucleic acid synthesis to biotechnology, pharmaceutical and synthesized nucleic acids. Both business units have service offerings as well, including genetic variation discoveryoligonucleotide synthesis companies and analysis services, novel chemistry development servicesresearch institutions throughout the world (the “Nucleic Acids Operating Segment”). In

the fourth quarter of 2005, we implemented a plan to exit the Nucleic Acids Operating Segment and custom synthesis of nucleic acids. Ourexpect to complete this plan during 2006.

Business Strategy

Since inception, our business strategy ishas been to align ourprovide products and services with the advancements in the field of genetics and to become a major supplier of products and services tobiomedical researchers, medical institutions, diagnostic and pharmaceutical companies. Specifically,companies that are tied to advancements in the field of genomics. Advances in genomics have fueled efforts to understand individual differences in disease susceptibility, disease progression, and response to therapy. Accordingly, a principal component of our strategy is to:has been to establish our WAVE

Our technologies center around three core competencies: separation chemistries, enzymology, and nucleic acid chemistries. We employ novel chemistries for separating nucleic acids, proteins, peptides, amino acids and carbohydrates. Our most significant separation technology is currently embodied in the WAVE System. The WAVE System is a versatile instrument that can be used for variation detection, size-based double-strand DNA separation and analysis, single-strand DNA separation and analysis and DNA purification. The WAVE System requires the use of various consumable products that we manufacture and sell separately.

Our second core competency is expertise in developing novel enzymes. Enzymes are proteins that act as catalysts for biochemical reactions. Several of these reactions are useful in genomics. The ability to develop enzymes useful in the experimental manipulation of genes provides powerful tools for producing genetic material in the form needed for further analysis or incorporation into diagnostics and therapeutics. These products can also expand the salesales of consumable products toused with the WAVE System users and may also be sold for other applications. Our SURVEYOR^® product line of mutation detection kits allow system and create opportunities to market additional products to this customer base. In addition, through our Discovery Services offerings, we have gained exposure to the translational and clinical research markets, laying the foundation for increasing our participation in the cleaving of DNA at points where DNA sequence variations exists. The resulting DNA fragments can then be analyzed by our WAVE System, fluorescent capillary electrophoresis or standard gel electrophoresis. SURVEYOR Kits provide a simple and robust method of scanning relatively large DNA fragments for both known and novel sequence variations.

Our third core competency is nucleic acid chemistries. Our synthetic nucleic acid products consist of chemical building blocks of nucleic acids (known as “phosphoramidites”), fluorescent markers and dyes, associated reagents, and synthesized segments of nucleic acids (known as “oligonucleotides” and “oligomimetics”). These products are used by research organizations, diagnostic companies and pharmaceutical companies. We produce these products in our Glasgow, Scotland facility and our Cgmp facility in Boulder, Colorado. The Boulder, Colorado facility is able to further process phosphoramidite products into synthesized oligonucleotides in larger quantities. This facility will also provide process development, enhancement and unique chemistry development services. Finally, our nucleic acid chemistry capabilities also include the ability to produce related specialty chemicals, such as molecular tags, dyes, quenchers, linkers, and solvents used to modify nucleic acids for subsequent detection or manipulation.

The Company’s operations are managed based upon the nature of the products and services provided. Accordingly, the Company operates in two reportable segments, BioSystems and Nucleic Acids. Operations for these segments are evaluated based upon specific identification of revenues and expensesfull value chain associated with the business activities resulting in a segment operating income.

Business Strategy

Our business strategy isranging from basic biomedical research to align our product and service offerings with the evolutiondevelopment of genetic advancements and to become a major supplier of products and services to researchers, medical institutions, diagnostic and pharmaceutical companies. Genetic advancements have developed and continue to develop over time. The movement in the field of genomics, and related market opportunities, has shifted from gene discovery to the analysis of variations in gene sequences. Researchers are beginning to link variations in the gene sequences to disorders and diseases. This knowledge may lead to the creation of diagnostic tests and the development of therapeutic treatments and drugs for these disorders and diseases.

Our Nucleic Acids segment has historically operated at a loss and produced negative cash flow. While we believe the long-term prospects for this business segment are favorable, the projected levels of near-term revenues from this segment are not expected to generate either positive cash flows or a profit from operations. After considering, amongst other factors, the historical financial results of this division and the near-term outlook for the nucleic acids industry, our Board of Directors directed management to explore strategic alternatives for this operating segment, including the possible sale of one or both of the facilities in Glasgow, Scotland and Boulder, Colorado. The process of exploring and evaluating alternatives for our Nucleic Acids segment is ongoing and no transaction has been agreed to as of the date hereof. However, it is possible that we may not continue to pursue the Nucleic Acid segment of our business as a result of this process.

products.

Sales and Marketing

We currently sellhave sold our products to customers in over 30 countries. We use a direct sales and support staff for sales in the U.S., U.K. and most countries in Western Europe. For the rest of the world, we sell our products through dealers and distributors located in those local markets. As of August 31, 2003, we hadWe have over 25 dealers and distributors. We also maintain regionally-based technical support staffs and applications scientists to support our sales and marketing activities throughout the U.S. and Europe.

Customers

Customers include numerous leading academic and medical institutions in the U.S. and abroad. In addition, our customers also include a number of large, established U.S. and foreign pharmaceutical, biotech and commercial companies. During the first six months of 2004, sales to Geron Corporation represented 10.2% of total consolidated revenue and 41.8% of total revenue within our Nucleic Acids business unit. No other customers currently accountcustomer accounts for more than 10% of total consolidated or segment revenue.

net sales.

Research and Development

We maintain an active program of research and development and expect to continue to incur significant expense for these activities going forward. Our research and development activities includeprimarily directed toward the improvement of the DNA separation media used in our WAVE System,^® system, the refinement of the hardware and software components of the WAVE System,^® system, the creation of unique enzymes and WAVE-Optimized^® enzymes, and the improvementdevelopment of chemical and biochemical reaction techniques for synthetic nucleic acids. Throughassays on the first six months of 2004, ourWAVE^® system.

We will need to continue to invest in research and development expenditures were approximately $3.6 million. This represents a substantial reduction fromactivities in order to remain competitive and to take advantage of new business opportunities as they arise. For the levels of expenditures in recent years. Ouryears ended December 31, 2005, 2004 and 2003, our research and development expenses were $9.3$2.20 million, $12.2$4.50 million and $9.4$6.83 million, in 2003, 2002 and 2001, respectively. We expect thatDuring the first quarter of 2006, we will further curtail ourincurred research and development activities until we are ableexpense of $0.6 million. We expect our total research and development expense during 2006 to increasebe approximately equal to the 2005 levels.

In addition to the amounts reflected above, our revenuesdiscontinued Nucleic Acids Operating Segment incurred no research and otherwise improve our liquiditydevelopment expenses during three months ended March 31, 2006 or the year ended December 31, 2005, but incurred $2.18 million and working capital positions.$2.47 million of research and development expenses during the years ended December 31, 2004 and 2003, respectively.

Manufacturing

We manufacture bioconsumable products including our separation columns, liquid reagents, enzymes and nucleic acid products.enzymes. The major components of our WAVE^® systems are manufactured for us by a third party. We integrate our own hardware and software with these third party manufactured components. Our manufacturing facilities for our WAVE^® systems and bioconsumables are located in Omaha, Nebraska, San Jose, California, and Cramlington, England. Our Synthetic Nucleic Acid products are manufactured in Glasgow, ScotlandThe nature of our instruments and Boulder, Colorado.

bioconsumables business does not generally lend itself to tracking and reporting sales backlog.

Intellectual Property

To establish and protect our proprietary technologies and products, we rely on a combination of patent, copyright, trademark and trade-secret laws, as well as confidentiality provisions in our contracts. We have successfully prosecuted or licensed in numerous patents protecting our core technologies, and as a result we presently own rights to more than 8040 issued patents and over 7020 pending applications in both the U.S. and abroad. Our DNA separation technologiesWAVE^® System and methods embodied in our BioSystems business unit productsrelated consumables, are protected by patents and licensed technologies. These patents, including licensedin-licensed technologies have remaining lives of

between 9 to 18 years. Intellectual property related to our Nucleic Acid business unit is mainly inlicensed.that expire in various periods beginning in 2013 through 2022. We expect towill continue to file patent applications and seek new licenses as wewarranted to protect and develop new technologies of interest to our customer base in the coming years.

Competition

The markets in which we operate are highly competitive and characterized by rapidly changing technological advances. A number of our competitors possess substantial resources and are able to develop and offer a much greater breadth of products and/or services, coupled with significant marketing and technologies.distribution capabilities. We compete principally on the basis of providing uniquely enabling technical advantages in specific but significant market segments.

Competition for our WAVE^® systems arises primarily from DNA sequencing and genotyping technologies. Competitors in these areas include Applied Biosystems, Beckman Coulter, Amersham (now part of GE Healthcare), Affymetrix, Agilent Technologies, Nanogen, Illumina, Sequenom, Pyrosequencing (now part of Biotage AB), Varian, and others. Competition for some of our non-WAVE^® consumable products comes from numerous well-diversified life sciences reagents providers, including, among others, Invitrogen, Qiagen, Roche, Stratagene, and Promega. Our discovery services product line faces competition from a number of companies offering contract DNA sequencing and other genomic analysis services, including Genaissance Pharmaceuticals, GeneLogic, Agencourt, SeqWright, Gentris, and Perlagen. In addition, several clinical diagnostics service providers, such as Labcorp, Quest, and Specialty Laboratories, also offer related laboratory services in support of clinical trials. Finally, additional competition arises from academic core laboratory facilities.

Recent DevelopmentsEvents

We have hired a new Chief Executive Officer

Craig Tuttle was appointed as our President and Chief Executive Officer on July 12, 2006. Mr. Tuttle succeeded our interim Chief Executive Officer, Michael Summers, who will continue to serve as our Chief Financial Officer. Mr. Tuttle, age 54, has over 25 years of general management, sales and marketing and research and development experience in medical diagnostic and biotechnology companies. During 2004 and 2005, Mr. Tuttle was the President and COO of Duke Scientific, a Northern California specialty chemistry manufacturer. Mr. Tuttle led the sale of Duke Scientific to Fisher Healthcare in 2005. From 1997 to 2003, Mr. Tuttle was with Apogent Technologies, Inc. where he served in various roles, including President of Applied Biotech, Inc., the manufacturer of the market leading home pregnancy test,

and General Manager at Seradyn, Inc., a specialty chemical and diagnostic test manufacturer. Mr. Tuttle earned a B.S in Biochemistry from UCLA, an M.S. in Biochemistry from the University of Colorado and an M.B.A from St. Mary’s College. We entered into an employment agreement with Mr. Tuttle which has a term of two years, but will be automatically extended for additional one-year periods unless either the Company or Mr. Tuttle elects not to further extend it. Under the terms of the Employment Agreement, Mr. Tuttle will be paid a base salary of $250,000 per year during the initial two-year term. His salary may increase in subsequent terms as determined by the compensation committee of our Board of Directors. Mr. Tuttle is also eligible to receive an annual bonus of up to 20% of his base salary and will receive allowances for a leased automobile, housing in the Omaha, Nebraska area and commuting costs for a period of one year. Subject to approval of the compensation committee, Mr. Tuttle will be granted options to purchase 200,000 shares of our common stock shortly after joining the Company, options to purchase 200,000 shares on January 12, 2007, and options to purchase 200,000 shares on July 12, 2007. Each such grant of options will vest equally on the next three anniversary dates of the respective grant. The Employment Agreement contains standard confidentiality and noncompetition provisions and provides for a severance payment to Mr. Tuttle equal to one year’s salary if he is discharged for reasons other than as defined in the Employment Agreement as “just cause”.

LiquidityWe amended our 1997 Stock Option Plan

On July 12, 2006, our stockholders approved the adoption of our new 2006 Equity Incentive Plan (the “2006 Plan”) which amended and replaced our Fourth Amended and Restated 1997 Stock Option Plan (the “1997 Plan”). DespiteThe 2006 Plan expands the types of equity compensation awards available to our effortscompensation committee to reduce costsinclude stock appreciation rights, restricted stock, restricted stock units, performance shares and performance units, as well as the qualified and non-qualified stock options that were previously available under the 1997 Plan. Under the 2006 Plan, the compensation committee will have more flexibility in designing compensation packages to obtain additional debthelp us attract and retain qualified officers, employees and directors. The 2006 Plan also increased the total number of shares of our common stock that may be issued as equity financing, our liquidity and working capital position has deteriorated.compensation from 7,000,000 to 10,000,000 shares. As of August 31, 2004, we had approximately $665,000 in cashJuly 12, 2006, options for a total of 6,263,533 shares have been issued under the 1997 Plan. The adoption of the 2006 Plan did not change the basis upon which the Compensation Committee awards equity compensation grants.

We decided to exit our former Nucleic Acids operating segment.

On December 22, 2005, the Company’s Directors voted to either sell or close and cash equivalents. The deterioration in our liquidity and working capital position is largely due toliquidate the operating losses that we continue to incur, particularly in our Nucleic Acids operating segment, which consists primarily of a manufacturing facility in Glasgow, Scotland. This decision was made after an evaluation of, among other things, short and long-term sales projections for products sold by this operating segment, including estimates of 2006 sales to increased accounts receivable (largely from international sales), inventory, and to a lesser extent, purchases of property and equipment. In particular, our Boulder, Colorado facility continues to generate significant negative cash flows from operations in the range of $200,000 to $300,000 per month.

operating segment’s largest customer. We have funded operating lossescommenced closure and other usesliquidation of liquidity primarily through increased borrowings under two loan arrangements entered into with Laurus Master Fund, Ltd. (“Laurus”). Inthe facility in Glasgow, Scotland. At March 31, 2006 and December 2003,31, 2005, we obtained a three-year $7.5had accrued expenses of $0.42 million line of credit facility from Laurus. Funds available under the line are determined by a borrowing base equal to 90% of eligible accounts receivable balances plus up to $1.0and $0.72 million related to inventory balances. However, Laurus has waived this borrowing limitation through March 19, 2005statutory payment to affected employees and other costs specifically attributable to closure of the facility. We expect to incur additional period costs attributable to closure of the facility that will be recorded in order to make the entire $7.5 million available to us. This line of credit is secured by mostdiscontinued operations during 2006.

We completed a private placement of our assets. Borrowings under this loan carry an interest ratecommon stock in the fourth quarter of 2.0% over the prime rate, subject2005.

On October 31, 2005, we issued securities to institutional investors in a minimum of 6.0% per annum. Payment of interest and principal can, under certain circumstances, be made withprivate placement (the “2005 Private Placement”). The securities issued consisted of: (i) 14,925,743 shares of the Company’s common stock. Conversionstock, plus (ii) five-year, non-callable warrants to purchase another 5,970,297 shares of this debt to common stock may be made atwith an exercise price of $1.20 per share. The aggregate purchase price for the election of Laurus or the Company. We may elect to convert borrowings into stock only if our shares trade at a price exceeding $1.10securities sold was

$1.01 per share for ten consecutive trading days and such conversion is further subjectof common stock initially being sold or $15.08 million. In conjunction with this transaction, we issued a warrant to trading volume limitations and a limitation on the total beneficial ownership by Laurus of our common stock. In orderOppenheimer & Co., Inc. to obtain an extension of the borrowing base waiver and certain other concessions, we amended the line of credit facility in August 2004 to reduce the fixed conversion price from $2.20purchase 932,859 shares at $1.20 per share to $1.00 per share. Asas part of September 10, 2004, we had $1.1 million available under this facility.their placement fee.

In February 2004, we entered into a separate $2.75 million convertible term note with Laurus. Portions of theThe net proceeds from thisthe 2005 Private Placement were $13.90 million after transaction costs of $1.18 million. These proceeds were mainlypartially used to retire the mortgage debtrepay all outstanding principal and accrued interest on our facilityloans to Laurus Master Funds, Ltd. (“Laurus”) including fees paid to Laurus to facilitate the 2005 Private Placement and prepayment penalties to Laurus in Glasgow, Scotland.the sum of $0.82 million. As a result, the Laurus loans have been cancelled and are no longer available to us. The remaining proceeds of approximately $750,000$5.35 million will be used for future working capital needs.

Liquidity and Capital Resources

We have experienced recurring net losses and had an accumulated deficit at March 31, 2006 of $122.40 million. To respond to changes in the overall business climate for our products, our liquidity position and capital structure, we have instituted significant change that began in the fourth quarter of 2004 with the sale of our specialty oligonucleotide manufacturing facility, a wide-reaching restructuring plan and the exit of our former Nucleic Acids Operating Segment.

Our working capital positions at March 31, 2006 and December 31, 2005 were usedas follows (in thousands):

While we believe that existing sources of liquidity are sufficient to furthermeet expected cash needs through 2006, we have experienced recurring net losses and have historically relied upon cash flows from investing and financing activities to offset significant cash outflows from operating activities. To the build-outextent necessary, we believe that we can manage costs and expenses at reduced levels to conserve working capital. The need for any such cost and expense reductions would likely delay implementation of the Glasgow facility, complete the consolidation of operations into the new facility and to provide funds for operations. The term note carries an interest rate of 2.0% over the prime rate, subject to a minimum of 6.0% per annum, and has a term of 3 years. The principal and interest on the term note may also be converted into our common stock. Inbusiness plan. Ultimately, we must achieve sufficient revenues in order to obtain certain concessions, we amended the term note in August 2004generate positive net earnings and cash flows from operations.

Shares to reduce the fixed conversion price from $2.61 per share to $1.00 per share.be sold by Selling Stockholders

In connection with the line of credit facility and term note, we issued warrants to Laurus to acquire 1,075,000This Prospectus covers 24,090,795 shares of our common stock at exercise prices ranging from $1.25 to $3.11 per share.

In order to meet our cash needs forthat the remainder of 2004, it is essential that we significantly reduce operating losses, particularly in our Nucleic Acids operating segment, either through increased revenues or further expense reductions. We have taken steps to further reduce our operating expenses, including reductions in workforce, furloughs, scaled back operations, consolidationselling stockholders listed under “Selling Stockholders” may offer and other cost containment measures, and we expect to continue to implement measures to reduce our need for operating cash. However, implementation of some of these measures, such as workforce reduction, could actually result in an increased demand for cash in the short-term. In addition, certain costs such as facility leases may not be renegotiated or terminated. Excess property and equipment resulting from future facility consolidation could be liquidated at prices that may or may not approximate book value. We could also delay capital expenditures to the extent possible to conserve cash.

We also continue to explore strategic alternatives with respect to our Nucleic Acids business segment. This operating segment primarily consists of two facilities, our oligonucleotides facility in Boulder, Colorado and our phosphoramidites manufacturing facility in Glasgow, Scotland. Potential strategic alternatives for our Nucleic Acids business include the sale of one or both of these facilities.

We are also working to improve the collection of accounts receivables. As of August 31, 2004, we have over $8.3 million invested in accounts receivable. However, our collection cycle, particularly in Europe, is relatively long and has lengthened due to

uncertainty in funding for capital spending among our customer base. In addition to focusing on accelerating collections, we may decide to factor or sell receivables not used as collateral under our loan facilities with Laurus. While this may generate additional cash, the receivables would have to be sold at significant discounts. We are also exploring liquidating raw materials or works in process inventories in our Nucleic Acids segment. As of August 31, 2004, we had over $5.8 million invested in these inventories. Although these inventories generally have a long shelf life, they may require reworkingresell from time to time. Alternatively, we may chooseThese shares consist of (i) 13,978,218 shares issued in conjunction with the 2005 Private Placement; (ii) 6,903,156 shares issuable upon the exercise of warrants that were also issued in conjunction with the 2005 Private Placement; (c) 2,050,000 shares issued in conjunction with a private placement that closed in the fourth quarter of 2003; and (iv) 1,159,421 shares issuable upon the exercise of outstanding warrants that were issued primarily in conjunction with our past indebtedness to liquidate someLaurus. The exercise price of these inventorieswarrants range from $1.20 to $3.18 per share. The selling stockholders are offering the common stock as described under “Plan of Distribution.”

At July 12, 2006, we had 49,189,672 shares issued and outstanding. The number of shares outstanding does not include (i) the 8,062,577 shares issuable upon the exercise of outstanding warrants

and (ii) up to 9,246,231 shares of our common stock that we could issue under our employee stock option plan, of which 5,475,264 options are outstanding at a significant discountJune 30, 2006.

Use of Proceeds

This Prospectus relates to market or book value.

The effectshares of our common stock that may be offered and sold from time to time by the selling stockholders. This Prospectus also relates to common stock issuable upon the exercise of warrants held by certain selling stockholders. We will not receive any proceeds from the sale of shares of common stock in this offering. We will, however, receive proceeds from the exercise of the executionwarrants, if exercised. The proceeds from the exercise of warrants, if any, of these items on our financial position, operations and cash flows has not been quantified but could be significant. Additionally, there is no assurance any of these steps will allow us to meet our cash needs or that we will be able to obtain additional debt or equity financing to meet future cash needs. If we are not able to meet our needsused for working capital we may not be able to execute parts or all of our business plan and may need to discontinue operations in one or both of our business segments.

purposes.

Impairment of Nucleic Acid Segment AssetsGENERAL INFORMATION. Based upon information obtained through the process of evaluating strategic alternatives for our Nucleic Acids segment, we determined that it was more likely than not that the value of these assets associated with this business were impaired. We engaged an external valuation firm to conduct an interim period impairment test which resulted in us recording a non-cash charge of $11,964,387 related to these assets during the three months ended June 30, 2004. The charge consisted of $9,864,387 related to the impairment of goodwill and $2,100,000 related to the impairment of property and equipment.

Changes in Senior Management. Michael A. Summers became our Chief Financial Officer effective August 17, 2004. Michael Summers replaced Mitchell Murphy who was acting as interim Chief Financial Officer since the departure of Michael Draper in March, 2004. Mr. Summers’ previous experience includes ten years in public accounting and five years at publicly traded companies. Mr. Murphy remains as Vice President, Secretary and Treasurer.

In addition, John Allbery, resigned as Executive Vice President of Operations in August, 2004 to pursue other business opportunities. Mr. Allbery had primary responsibility for oversight of the Company’s Nucleic Acids business segment. Collin D’Silva, our Chief Executive Officer, has assumed these responsibilities.

New Litigation. In August, 2004, we were notified that we were the defendant in a lawsuit brought by a prospective distributor of our products located in Spain. The plaintiff claims that we breached a promise to award a distributorship to him for a specific geographic area and is seeking monetary relief of approximately $500,000. We believe we have viable defenses to the plaintiff’s claims and intend to defend this lawsuit vigorously.

General Information

We were incorporated in Delaware on March 6, 1997. Our principal office is located at 12325 Emmet Street, Omaha, Nebraska 68164 (telephone: 402-452-5400). We maintain manufacturing facilities in Omaha, Nebraska, Boulder, Colorado, San Jose, California Glasgow, Scotland and Cramlington, England. We maintain research and development offices in Gaithersburg, Maryland Boulder, Colorado, Piscataway, New Jersey and Omaha, Nebraska.

Our internet address iswww.transgenomic.com. We make our annual report on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K and amendments to those reportsfiled by us with the SEC available free of charge throughon our website as soon as reasonably practicable after we file these documents with the Securities and Exchange Commission.reports are filed. The information contained inaddress of our website is www.transgenomic.com. Information on our website, including any SEC report, is not part of this Prospectusprospectus and you should not rely on it in deciding whether to invest in our common stock.

RISK FACTORS

An investment in our common stock involves a number of risks. Before making an investment decision, you should carefully consider all of the risks described in this Prospectus and the documents that are incorporated by reference into this Prospectus. The risks discussed in this Prospectus could materially adversely affect our business, financial condition and results of operations and cause the trading price of our common stock to decline significantly. If this occurs, you may lose all or part of your investment.

Risks Relating to Our Business

We may not have adequate financial resources to execute our business plan and may be need to terminate some operations.plan.

Despite our efforts to reduce costs and to obtain additional debt and equity financing, our liquidity and working capital position has deteriorated. As of AugustAt March 31, 2004,2006, we had approximately $665,000 in cash and cash equivalents. The deterioration in ourequivalents of $6.6 million. While we believe that existing sources of liquidity are sufficient to meet expected cash needs through 2006, we have experienced recurring net losses and working capital position is largely duehave an accumulated deficit totaling $122.4 million at March 31, 2006 and have historically relied upon cash flows from investing and financing activities to offset significant cash outflows from operating activities. To the operating lossesextent necessary, we believe that we continuecan manage costs and expenses at reduced levels to incur, particularlyconserve working capital. The need for any such cost and expense reductions would likely delay implementation of our business plan. Ultimately, we must achieve sufficient revenues in our Nucleic Acids operating segment, and to increased accounts receivable (largely from international sales), inventory, and to a lesser extent, purchases of property and equipment. We expect to continue to need substantial amounts of cash to fund our operations and capital expenditures and our existing cash balances, cash generated by operations, and our remaining borrowing capacity under our existing line of credit may be insufficient to satisfy our liquidity requirements. In order to meet ourgenerate positive net earnings and cash needs for the remainder of 2004, it is essential thatflows from operations. However, we significantly reduce operating losses, particularly in our Nucleic Acids operating segment, either through increased revenues or further expense reductions. We also need to accelerate the collection of accounts receivables and eliminate or delay capital expenditures. There is no assurance any of these steps will allow us to meet our cash needs. In addition, there is no assurancecannot assure you that we will be able to obtain additional debt or equity financing to meet future cash needs. If we are not able to meetincrease our needs for working capital, we may not be able to execute parts or all of our business plan and may need to discontinue operations in one or both of our business segments.

revenues.

We have a history of operating losses and expect tomay incur losses in the future.

We have experienced losses from continuing operations since inception of our operations. Our operating lossesloss from continuing operations for each of the last three fiscalmonths ended March 31, 2006 was $0.30 million. Losses from continuing operations for the years ended December 31, 2005, 2004 and 2003 were $22.6$4.98 million, $21.7$13.75 million, and $9.7$9.56 million, in 2003, 2002 and 2001, respectively, and for the first six months of 2004 were $18.0 million.respectively. These losses have been due principally to the high levels of research and development expenses and sales and marketing expenses that we have incurred in order to develop and market our products, restructuring charges and impairment charges. In addition, markets for our products have developed more slowly than expected in many cases and may continue to do so. As a result, we expect tomay incur operating losses in the future and we may never be profitable.

We may issue a substantial amount of our stock in conversion of our debt and exercise of options and warrants and this could reduce the market price for our stock.

As of August 30, 2004, we had outstanding approximately 29.1 million shares of common stock. We also had obligations to issue approximately 6.6 million million shares of common stock under outstanding stock options and warrants. Additionally, we may issue shares of common stock upon conversion of all or part of our line of credit and convertible tern note with Laurus. Currently, Laurus may acquire 5,750,000 shares of our common stock upon conversion of this debt. The issuance of such additional shares of common stock may be dilutive to our current shareholders and could negatively impact the market price of our common stock.

future.

Markets for our products and services may develop slowly.

There are many factors that affect the market demand for our products and services that we cannot control. This is especially true in our Nucleic Acid segment where the demand for our products depends to a large degree on the success that our customers and potential customers have in developing useful pharmaceutical products based on genetic intervention. A central strategy for our Nucleic Acid segment is to sell synthetic nucleic acid products to biopharmaceutical and pharmaceutical companies that are seeking to develop commercially viable genomic-based diagnostic and therapeutic products. We have invested a significant amount of capital into acquiring and developing manufacturing facilities and other assets to allow us to pursue this market. However, this is a new field of commercial development, and many of these biopharmaceutical and pharmaceutical companies are in the early stages of their efforts to develop genomic-based diagnostics and therapeutics and have encountered difficulties in these efforts. As a result, the demand for our synthetic nucleic acid products is difficult to forecast and may develop slowly or sporadically. In addition, we cannot assure you that these companies will not internally develop the chemistries and manufacturing capabilities to produce the products they could buy from us. Demand for our WAVE System^® system is similarly affected by the needs and budgetary resources of research institutions, universities, hospitals and others who use the WAVE System^® system for genetic-variation research. The WAVE System^® system represents a significant expenditure by these types of customers and often requires a long sales cycle. If revenues from the sales of our products and services continue at current levels, we may need to take steps to further reduce operating expenses or raise additional

working capital. We cannot assure you that sales will increase or that we will be able to reduce operating expenses or raise additional working capital.

A single customer accounts forSales of Discovery Services depend upon a significant portionsmall number of the sales in our Nucleic Acids business segment.customers and may fluctuate greatly.

DuringSales of Discovery Services tend to be made pursuant to large contracts and other arrangements with a small number of customers. As a result, revenues related to Discovery Services may be subject to substantial fluctuation, as the first six monthsgain or loss of 2004, approximately 42% of the total revenues generated by our Nucleic Acids segment represented sales to a single customer Geron Corporation. We do not have a long-term sales agreement with Geron Corporation and, accordingly, the amount of nucleic acid products we sell to it is subject to change. Revenues from our Nucleic Acids business would be substantially reduced if Geron Corporation’s need for our products declined or if it decided to obtain these products from other suppliers.

Customer clinical trials may be delayed or discontinued.

A significant percentage of our Nucleic Acid business unit revenues are generated by sales to customers involved in drug development. Our products are generally used by these customers in the manufacture of drugs candidates in varying stages clinical trials. If these clinical trials are delayed or cancelled or are otherwise not successful, this could have a significant impact on revenues generated by our Nucleic Acid business unit.such revenues.

The sale of our products and business operations in international markets subjects us to additional risks.

During the last three fiscalpast several years, our international sales have been approximately 50-65%represented more than half of our total net sales. As a result, a major portion of our revenues and expenses are subject to risks associated with international sales and operations. These risks include:

Our WAVE System^® system includes hardware components and instrumentation manufactured by a single supplier and if we are no longer able to obtain these components and instrumentation our ability to manufacture our products could be impaired.

We currently rely on a single supplier, Hitachi High Technologies America, to provide the basic instrument used in our WAVE Systems.^® systems. While other suppliers of instrumentation and computer hardware are available, we believe that our arrangement with Hitachi offers strategic advantages. Hitachi is replacing its current instrument line with a new instrument line. While we presently plan to convert our technology and applicationapplications to this new instrument line, such conversion may not be successful and, therefore, we may incur additional costs for the custom manufacturing of the current instrument line. If we were required to seek alternative sources of supply, it could be time consuming or expensive or require significant and costly modification of our WAVE System.^® system. Also, if we were unable to obtain instruments from Hitachi in sufficient quantities or in a timely manner, our ability to manufacture our products could be impaired, which could limit our future revenues.

We may not have adequate personnel to execute our business plan.

In order to reduce our operating costs, we have significantly reduced ourthe number of employees, including reductions in our research and development staff and our sales and marketing personnel. In addition, we may lose other key management, scientific, technical, sales and manufacturing personnel from time to time. It may be very difficult to replace personnel if they are needed in the future, and the loss of key personnel could harm our business and operating results. We cannot assure you that our employee reductions will not impair our ability to continue to develop new products and refine existing products in order to remain competitive. In addition, these reductions could prevent us from successfully marketing our products and developing our customer base.

Our markets are very competitive.

We compete with many other companies in both our Biosystems segment and Nucleic Acids segment. Competitors for our Biosystems segment include several companies, such as Varian, Waters, Agilent, Applied Biosystems, Beckman Coulter, Amersham Biosciences and Invitrogen. These companies provide various products and services that compete either directly with our WAVE system, bioconsumables and services, or indirectly through alternative technologies and/or methods. Competitors for our Nucleic Acid segment vary depending on the product. In the standard chemical building blocks market, we compete with Applied Biosystems, Proligo Degussa and Pierce Nucleic Acid Technologies. The competitors for our pharmaceutical-grade oligonucleotide synthesis products and services include primarily Proligo Degussa, Dow Chemical and Avecia. Many of these competing companiesour competitors have greater resources than we do and/or may enjoy other competitive advantages. This may allow them to more effectively market their products to our customers or potential customers, to develop products that make our products obsolete or to produce and sell products

less expensively than us. As a result of these competitive factors, demand for and pricing of our products and services could be negatively affected.

The price for our common stock is volatile and may drop further.

The trading price for our stock has fluctuated significantly over recent years. The volatility in the price of our stock is attributable to a number of factors, not all of which relate to our operating results and financial position. Nevertheless, continued volatility in the market price for our stock should be expected and we cannot assure you that the price of our stock will increase in the future. Fluctuations or further declines in the price of our stock may affect our ability to sell shares of our stock and to raise capital through future equity financing.

If we are unable to maintain our Nasdaq listing, your ability to trade shares of our common stock could suffer.

In order for our common stock to remain listed on the Nasdaq Stock Market, we must meet the minimum listing requirements for continued listing, including, among other requirements, minimum bid price and market value of public float requirements. If we fail to continue to meet the minimum listing requirements, we may be delisted from the Nasdaq. If our common stock is delisted from the Nasdaq, transactions in our common stock would likely be conducted only in the over-the counter market, or potentially on regional exchanges, which could negatively impact on the trading volume and price of our common stock, and investors may find it more difficult to purchase or dispose of, or to obtain accurate quotations as to the market value of, our common stock. In addition, if our common stock were not listed on the Nasdaq and the trading price of our common stock fell below $1.00 per share, trading in our common stock would also be subject to the requirements of certain rules which require additional disclosures by broker-dealers in connection with any trades involving a stock defined as a “penny stock.” In such event, the additional burdens imposed on broker-dealers to effect transactions in our common stock could further limit the market liquidity of our common stock and the ability of investors to trade our common stock.

Our patents may not protect us from others using our technology that could harm our business and competitive position.

Patent law relating to the scope of claims in the technology fields in which we operate is still evolving. The degree of future protection for our proprietary rights is uncertain. Furthermore, we cannot be certain that others will not independently develop similar or alternative products or technology, duplicate any of our products, or, if patents are issued to us, design around the patented products developed by us. Our patents or licenses could be challenged by litigation and, if the outcome of such litigation were adverse to us, our competitors could be free to use our technology. We may not be able to obtain additional patents for our technology, or if we are able to do so, patents may not provide us with substantial protection or be commercially beneficial. In addition, we could incur substantial costs in litigation if we are required to defend ourselves in patent suits brought by third parties or if we initiate such suits.

We cannot be certain that other measures taken to protect our intellectual property will be effective.

We rely upon trade secret protection, copyright and trademark laws, non-disclosure agreements and other contractual provisions for some of our confidential and proprietary information that is not subject matter for which patent protection is being sought. Such measures, however, may not provide adequate protection for our trade secrets or other proprietary information. If theysuch measures do not protect our rights, third parties could use our technology and our ability to compete in the market would be reduced.

We are dependent upon our licensed technologies and may need to obtain additional licenses in the future to offer our products and remain competitive.

We have licensed key components of our technologies from third parties. If these agreements were to terminate prematurely due to our breach of the terms of these licenses or we otherwise fail to maintain our rights to such technology, we may lose the right to manufacture or sell a substantial portion of our products. In addition, we may need to obtain licenses to additional technologies in the future in order to keep our products competitive. If we fail to license or otherwise acquire necessary technologies, we may not be able to develop new products that we need to remain competitive.

The patent underlying our nonexclusive license to manufacture standard nucleic acid building blocks will expire in the first quarter of 2005. The expiration of this patent could result in additional manufacturers entering the market for these products. Some of these manufacturers may have lower cost structures or other competitive advantages which may reduce our market share and/or our operating margins related to these products.

The protection of intellectual property in foreign countries is uncertain.

A significant percentage of our sales are to customers located outside the U.S. The patent and other intellectual property laws of some foreign countries may not protect our intellectual property rights to the same extent as U.S. laws. We may need to bring proceedings to defend our patent rights or to determine the validity of our competitors’ foreign patents. These proceedings could result in substantial cost and diversion of our efforts. Finally, some of our patent protection in the U.S. is not available to us in foreign countries due to the laws of those countries.

Our products could infringe on the intellectual property rights of others.

There are a significant number of U.S. and foreign patents and patent applications submitted for technologies in, or related to, our area of business. As a result, any application or exploitation of our technology could infringe patents or proprietary rights of others and any licenses that we might need as a result of such infringement might not be available to us on commercially reasonable terms, if at all. This may lead others to assert patent infringement or other intellectual property claims against us.

Our failure to comply with any applicable government regulations or otherwise respond to claims relating to improper handling, storage or disposal of hazardous chemicals that we use may adversely affect our results of operations.

Our research and development and manufacturing activities involve the controlled use of hazardous materials and chemicals. We are subject to federal, state, local and localinternational laws and regulations governing the use, storage, handling and disposal of hazardous materials and waste products. If we fail to comply with applicable laws or regulations, we could be required to pay penalties or be held liable for any damages that result and this liability could exceed our financial resources. We cannot assure you that accidental contamination or injury will not occur. Any such accident could damage our research and manufacturing facilities and operations, resulting in delays and increased costs.

Risks Relating To This Offering and Ownership of Our Common Stock

The price for our common stock is volatile and may drop.

The trading price for our common stock has fluctuated significantly over recent years. The volatility in the price of our stock is attributable to a number of factors, not all of which relate to our operating results and financial position. Nevertheless, continued volatility in the market price for our stock should be expected and we cannot assure you that the price of our stock will not decrease in the future. Fluctuations or further declines in the price of our stock may affect our ability to sell shares of our stock and to raise capital through future equity financing.

If we are unable to maintain our Nasdaq listing, your ability to trade shares of our common stock could suffer.

In order for our common stock to remain listed on the Nasdaq National Market (“Nasdaq”), we must meet the minimum listing requirements for continued listing, including, among other requirements, minimum bid price and market value of public float requirements. On February 15, 2006, we were notified that the bid price for our common stock over a 30-day period was below the $1.00 minimum required for continued listing of our common stock on the Nasdaq. In order to remain listed, the minimum bid price for our common stock must be at least $1.00 per share over ten consecutive business days before August 14, 2006. If we are not able to regain compliance with this listing requirement, we may be delisted from the Nasdaq. If our common stock is delisted from the Nasdaq, transactions in our common stock would likely be conducted only in the over-the counter market, or potentially on regional exchanges, which could negatively impact the trading volume and price of our common stock, and investors may find it more difficult to purchase or dispose of, or to obtain accurate quotations as to the market value of, our common stock. In addition, if our common stock were not listed on the Nasdaq and the trading price of our common stock fell below $1.00 per share, trading in our common stock would also be subject to the requirements of certain rules which require additional disclosures by broker-dealers in connection with any trades involving a stock defined as a “penny stock.” In such event, the additional burdens imposed on broker-dealers to effect transactions in our common stock could further limit the market liquidity of our common stock and the ability of investors to trade our common stock.

We may issue a substantial amount of our common stock to holders of options and warrants and this could reduce the market price for our stock.

At June 30, 2006, we had obligations to issue 13,537,841 shares of common stock including outstanding stock options representing 5,475,264 shares and warrants representing 8,062,577 shares. In addition, on July 12, 2006, our stockholders approved the adoption of our 2006 Equity Incentive Plan which amended our previous Fourth Amended and Restated 1997 Stock Option Plan to increase the total number of common shares that we may issue as equity compensation to our officers, directors and

employees from 7,000,000 to 10,000,000. The issuance of additional shares of common stock may be dilutive to our current stockholders and could negatively impact the market price of our common stock.

Our common stock is thinly traded and a large percentage of our shares are held by a small group of unrelated, institutional owners.

At July 12, 2006, we had 49,189,672 shares of common stock outstanding. Fewer than ten unrelated, institutional holders own a majority of these shares. The sale of significant shares into the public market has potential to cause significant downward pressure on the price of our common stock. This is particularly the case if the shares being placed into the market exceed the market’s ability to absorb the stock. Such an event could place further downward pressure on the price of our common stock. This presents an opportunity for short sellers to contribute to the further decline of our stock price. If there are significant short sales of our stock, the price decline that would result from this activity will cause the share price to decline more so, which, in turn, may cause long holders of the stock to sell their shares thereby contributing to sales of stock in the market.

The price you pay for shares offered by the selling stockholders may be higher than the prices paid by other people acquiring such shares.

Selling stockholders may sell shares under this Prospectus from time to time either at prices then prevailing in the market or at other prices they negotiate with buyers. Accordingly, the price you pay for shares of our common stock you purchase from a selling stockholder may be higher than the prices paid by other people acquiring such shares.

USE OF PROCEEDS

We will not receive any proceeds from the sale of the shares of common stockShares offered by this Prospectus. However, we received initial loan proceeds of $2.75 million on a 3 year term note which may be converted into 2,750,000 of the shares that may be offered hereby. Additionally, we have approximately $6.4 million outstanding on our line credit of which $3.0 million relates to a Secured Convertible Minimum Borrowing Note which may be converted into 3,000,000 of the shares that may be offered hereby. Another 909,091 shares were issued by us upon conversion of a previous $2.0 million Secured Convertible Minimum Borrowing Note issued pursuant to our line of credit, and these shares may also be sold hereunder. We previously received net proceeds of approximately $4.2 million pursuant to a Securities Purchase Agreement entered into with certain selling stockholders who may sell up to 4,500,000 shares hereunder. Finally, we will receive approximately $2.4$10.49 million upon the exercise of warrants for the remaining 1,136,484 shares8,062,577 Shares that may be offered hereby. The loan proceeds, the proceeds from the sale of shares and thenet proceeds we receive from any exercise of these warrants, have been, orif any, will be used by us primarily for working capital purposes.

SELLING STOCKHOLDERS

The shares offered by this Prospectus may be sold from time to time by the selling stockholders named in the following table. The number of shares these selling stockholders are offering under this Prospectus will be adjusted to reflect any additional shares of common stock which may become issuable to the selling stockholders by reason of any stock dividend, stock split or other similar transaction effected without the receipt of consideration and which results in an increase in the number of our outstanding shares of common stock or which otherwise increases the number of shares issuable upon conversion of the loan proceeds or upon the exercise of the warrants under which such shares may by issued.

The following table also sets forth the total number of shares of our common stock beneficially owned by each of the selling stockholders and the percentage of our total outstanding shares of common stock that each selling stockholder beneficially owns. Percentage ownership is based on the shares of our common stock outstanding as of the date of this Prospectus plus the shares that may be issued to certain of the selling stockholders and which may be sold under this Prospectus. The estimate of shares owned after this offering assumes that all shares offered by the Prospectus are sold. These estimates may prove to be inaccurate because the selling stockholders may offer all or some of their shares and because there currently are no agreements, arrangements or understandings with respect to the sale of any of the shares.

		Shares Beneficially Owned Prior to the Offering							Shares Beneficially Owned After the Offering
Name		Number		Percentage			Shares to be Sold		Number		Percentage
Laurus Master Fund, Ltd.(1)		1,526,813		4.99	%		7,809,375		0		*
TN Capital Equities, Ltd.(2)		61,484		*			61,484		0		*
Mazama Capital Management, Inc.(3)
Advisors Fund for Employees Benefit Trust		14,100		*			14,100		0		*
The Collins Foundation		1,650		*			1,650		0		*
Daughters of Charity Fund—P		42,400		*			42,400		0		*
East Bay Municipal Utility District		20,200		*			20,200		0		*
Hendrix College		4,600		*			4,600		0		*
Horace Mann Small Cap Growth Fund		15,300		*			15,300		0		*
Intermountain Health Care		36,800		*			36,800		0		*
Kansas City Firefighters Retirement System		15,000		*			15,000		0		*
Los Angeles County Employee Retirement Association		264,213		*			264,213		0		*
Marin County Employee Retirement System		35,700		*			35,700		0		*
Mass Mutual Small Company Growth Fund		72,000		*			72,000		0		*
Northwest Airlines—DB		92,000		*			92,000		0		*
Northwest Airlines—DC		105,300		*			105,300		0		*
City of New York Police Pension Fund		76,600		*			76,600		0		*
Operf		26,184		*			26,184		0		*
Portland General Electric		13,600		*			13,600		0		*
Les Schwab Tires		13,300		*			13,300		0		*
SEI Institutional Investments Trust		144,900		*			144,900		0		*
SEI Institutional Managed Trust		246,400		*			246,400		0		*
University of Miami Growth Plan		39,000		*			39,000		0		*
Retirement Plan for University of Miami		22,300		*			22,300		0		*
Undiscovered Managers Small Cap Growth Fund		167,700		*			167,700		0		*
Utah Retirement Systems		144,200		*			144,200		0		*
Horizon Rudder & Co.		53,500		*			53,500		0		*
Subtotal—Mazama Capital Management, Inc.		1,666,947		5.73	%		1,666,947		0		*
Kopp Emerging Growth Fund(4)		2,800,000		9.63	%		2,050,000		750,000		1.84	%
Frank Colen		12,500		*			12,500		0		*
Edward Newman		0		*			0		0		*
James Irvine		0		*			0		0		*
		6,067,744		19.79	%		11,600,306		750,000		1.84	%

(2)

Shares to be sold consist of 1,075,000 shares issuable upon the exercise of warrants. The warrants are subject to a conversion cap which precludes the holder thereof from exercising such warrants to the extent that such owner would beneficially own in excess of 4.99% of the Company’s common stock. However, Laurus Master Funds,Fund Ltd. has contractually agreed to beneficial ownership limitations that restrict the conversion or exercise of securities held by Laurus to 4.99% of outstanding shares. However, they may elect to waive the 4.99% limitation with 75 days notice or upon default under the Convertible Term Note or the Senior Secured Convertible Minimum Borrowing Note. Shares to be sold consist of 3,265,625 shares issuable upon conversion of a $2.75 million Convertible Term Note, 3,468,750 shares issuable upon the conversion of a $3.0 million Secured Convertible Minimum Borrowing Note and 1,075,000 shares issuable upon the exercise of warrants.notice.

Each selling stockholder acquired, or will acquire, the shares to be sold by such selling stockholder in the ordinary course of business and, at the time of acquisition of such shares, no selling stockholder had any agreement or understanding, directly or indirectly, to distribute such shares.

PLAN OF DISTRIBUTION

The selling stockholders and any of their pledges, assignees, donees selling shares received from such selling stockholders as a gift, and successors-in-interest may, from time to time, sell any or their donees or pledgees may sellall of their shares of our common stock from time to time. The selling stockholders will act independently of uson any stock exchange, market or trading facility on which the shares are traded or in making decisions regarding the timing, manner and size of each sale. Theprivate transactions. These sales may be made on the Nasdaq National Market, in the over-the-counter marketat fixed or otherwise, at prices and terms then prevailing or at prices related to the then current market price, or in negotiated transactions. The last reported sale price of our common stock on September 13, 2004 was $1.16 per share.prices. The selling stockholders may effect such transactions by selling the shares to or through broker-dealers. The shares may be sold byuse any one or more of or a combination of, the following:following methods when selling shares:

The selling stockholders may also sell shares under Rule 144 under the Securities Act of 1933, as amended, if available, rather than under this prospectus.

To the extent required, this Prospectus may be amended or supplemented from time to time to describe a specific plan of distribution. In effecting sales, broker-dealersBroker-dealers engaged by the selling stockholders may arrange for other broker-dealers to participate in sales. Broker-dealers may receive commissions or discounts from the resales. The selling stockholders may enter into hedging transactions with broker-dealers in connection with distributions(or, if any broker-dealer acts as agent for the purchaser of the shares, or otherwise. In these transactions, broker-dealers may engage in short sales of the shares in the course of hedging the positions they assume with selling stockholders. The selling stockholders also may sell shares short and redeliver the shares to close out such short positions. The selling stockholders may enter into option or other transactions with broker-dealers which require the delivery to the broker-dealer of the shares. The broker-dealer may then resell or otherwise transfer such shares under this prospectus. The selling stockholders also may lend or pledge their shares to a broker-dealer. The broker-dealer may sell the shares so lent, or upon a default the broker-dealer may sell the pledged shares under this Prospectus.

Broker-dealers or agents may receive compensation in the form of commissions, discounts or concessions from selling stockholders. Broker-dealers or agents may also receive compensation from the purchasers of the shares for which they act as agents or to whom they sell as principals, or both. Compensation as to a particular broker-dealer might be in excess of customary commissions and will bepurchaser) in amounts to be negotiatednegotiated. The selling stockholders do not expect these commissions and discounts to exceed what is customary in connection with the sale. Broker-dealerstypes of transactions involved.

The selling stockholders and any broker-dealers or agents and any other participating broker-dealers orthat are involved in selling the selling stockholdersshares may be deemed to be “underwriters” within the meaning of Section 2(11) of the Securities Act of 1933 (the “Securities Act”) in connection with sales of the shares. Accordingly,such sales. In such event, any such commission, discount or concessioncommissions received by themsuch broker-dealers or agents and any profit on the resale of the shares purchased by them may be deemed to be underwriting discountscommissions or commissionsdiscounts under the Securities Act. Because selling stockholders may be deemed

We are required to be “underwriters” withinpay all fees and expenses incident to the meaning of Section 2(11)registration of the Securities Act,shares, including certain fees and disbursements of counsel to the selling stockholders. We have agreed to indemnify the selling stockholders will be subject to the prospectus delivery requirements ofagainst certain losses, claims, damages and liabilities, including liabilities under the Securities Act. In addition, any securities covered by

To the extent required, we will amend or supplement this Prospectus which qualify for sale under Rule 144 promulgated under the Securities Act may be sold under Rule 144 rather than under this Prospectus. The selling stockholders have advised us that they have not entered into any agreements, understandings orprospectus to disclose material arrangements with any underwriters or broker-dealers regarding the saleplan of their securities. There is no underwriter or coordinating broker acting in connectiondistribution.

To comply with the proposed salesecurities laws of shares by the selling stockholders.

The shares will be sold only throughcertain jurisdictions, registered or licensed brokers or dealers if required under applicable state securities laws. In addition, in certain statesmay need to offer or sell the shares may not be sold unless they have been registered or qualified for sale in the applicable state or an exemption from the registration or qualification requirement is available and is complied with.

Underoffered by this prospectus. The applicable rules and

regulations under the Securities Exchange Act of 1934, (the “Exchange Act”),as amended, may limit any person engaged in thea distribution of the shares may not simultaneouslyof common stock covered by this prospectus in its ability to engage in market making activities with respect to our common stocksuch shares. A selling stockholder, for a period of two business days prior to the commencement of such distribution. In addition, each selling stockholderexample, will be subject to applicable provisions of the Exchange Act and the associated rules and regulations under the Exchange Act, including Regulation M,it, which provisions may limit the timing of purchases and sales of any shares of our common stock by thethat selling stockholders. We will make copies of this Prospectus available to the selling stockholders and have informed them of the need to deliver copies of this Prospectus to purchasers at or prior to the time of any sale of the shares.

We will file a supplement to this Prospectus, if required, to comply with Rule 424(b) under the Securities Act upon being notified by a selling stockholder that any material arrangements have been entered into with a broker-dealer for the sale of shares

through a block trade, special offering, exchange distribution or secondary distribution or a purchase by a broker or dealer. Such supplement will disclose:

In addition, upon being notified by a selling stockholder that a donee or pledgee intends to sell more than 500 shares, we will file a supplement to this Prospectus.

We will bear all costs, expenses and fees in connection with the registration of the shares. We agreed to indemnify and hold the selling stockholders harmless against certain liabilities under the Securities Act that could arise in connection with the sale by the selling stockholders of the shares. The selling stockholders will bear all commissions and discounts, if any, attributable to the sales of the shares. The selling stockholders may agree to indemnify any broker-dealer or agent that participates in transactions involving sales of the shares against certain liabilities, including liabilities arising under the Securities Act.

stockholder.

EXPERTS

The consolidated financial statements as of December 31, 2003 and 2002 and for each of the three years in the period ended December 31, 2003 incorporated in this Prospectusprospectus by reference from ourthe Company’s Annual Report on Form 10-K for the year ended December 31, 2003 have been audited by Deloitte & Touche LLP, an independent registered public accounting firm, as stated in their report, (which report expresses an unqualified opinion and includes an explanatory paragraph relating to our receipt of a waiver of the borrowing base limit on our existing line of credit and a convertible note agreement in the first quarter of 2004 and our change in method of accounting for goodwill and other intangible assets in connection with the adoption of Statement of Financial Accounting Standards No. 142,Goodwill and Other Intangible Assets,in 2002), which is incorporated herein by reference, and hashave been so incorporated in reliance upon the report of such firm given upon their authority as experts in accounting and auditing.

LEGAL OPINIONS

The validity of the common stock offered by this Prospectus has been passed upon for us by Kutak Rock LLP, Omaha, Nebraska.

WHERE YOU CAN FIND MORE INFORMATION

We file annual, quarterly and special reports, proxy statements and other information with the Securities and Exchange Commission (the “SEC”).SEC. You may read and copy the materials we file at the SEC’s Public Reference Room at 450 Fifth100 F Street, N.W.N.E., Washington, D.C. 20549, as well as at the SEC’s regional office at Citicorp Center, 500 West Madison Street, Room 1400, Chicago, Illinois 60661-2511.20549. Please call the CommissionSEC at 1-800-SEC-0330 for further information on the operation of the Public Reference Rooms.Room. Our SEC filings are also available to the public on the Internet from the SEC’s World Wide Web site on the Internet at http://www.sec.gov. This site contains reports, proxy and information statements and other information regarding issuers that file documents electronically with the SEC.

We maintain a site on the World Wide Web at www.transgenomic.com. The information contained in our website is not part of this Prospectus and you should not rely on it in deciding whether to invest in our common stock.

We have filed numerous Registration Statements on Form S-3 (Registration Nos. 333-108319, Registration Nos. 333-111442, Registration Nos. 333-114661 and Registration Nos. 333-            ),a registration statement, of which this Prospectusprospectus is a part, covering the securities offered hereby. As allowed by SEC rules, this Prospectusprospectus does not containinclude all of the information set forthcontained in these Registration Statementsthe registration statement and

the exhibits, financial statements and schedules thereto. We refer you to these Registration Statements,the registration statement, and the exhibits, financial statements and schedules thereto, for further information. This Prospectusprospectus is qualified in its entirety by such other information.

INCORPORATION OF CERTAIN DOCUMENTSINFORMATION BY REFERENCE

The SEC allows us to “incorporate by reference” the information intowe file with them, which means:

We filed separately by usthe following documents with the SEC under the Securities Exchange Act of 1934 (the “Exchange Act”). The information incorporatedand incorporate them by reference is deemed to be part ofinto this Prospectus, except for any information superseded by information in this Prospectus. We have filed our annual reportProspectus:

Any documents we file pursuant to SectionSections 13(a), 13(c), 14 or 15(d) of the Exchange Act after the date of this Prospectus and prior to the termination of the offering of the securities to which this Prospectus relates will automatically be deemed to be incorporated by reference into this Prospectus and to be part hereof from the date of filing those documents. Any documents we file pursuant to these sections of the Exchange Act after the date of the registration statement that contains this Prospectus and prior to the effectiveness of the registration statement will automatically be deemed to be incorporated by reference into this Prospectus and to be part hereof from the date of filing those documents. In no event, however, will any of the information that we “furnish” to the SEC in any Current Report on Form 8-K from time to time be incorporated by reference into, or otherwise included in, this Prospectus.

Any statement contained in this Prospectus or in aany document incorporated, or deemed to be incorporated, by reference into this Prospectus shall be deemed to be modified or superseded for all purposes of this Prospectus to the extent that a statement contained in this Prospectus or in any othersubsequently filed document whichthat also is alsoor is deemed to be incorporated by reference into this Prospectus modifies or supersedes thatsuch statement. Any statement so modified or superseded shall not be deemed, except as so modified or superseded, to constitute a part of this Prospectus and the related registration statement.

You maycan obtain copiesany of all documents which are incorporated in this Prospectus by reference (other than the exhibits to those documents which are not specificallyour filings incorporated by reference herein)into this Prospectus from us or from the SEC on the SEC’s Web site at the address listed above. We will provide without charge to each person to whom this Prospectus is delivered, upon written or oral request, a copy of these filings or portions of these filings by writing or calling Mr. Mitchell L. Murphy, at telephoning:

Michael A. Summers

Transgenomic, Inc.,

12325 Emmet Street

Omaha, NE 68164 telephone number (402) 452-5400.

402-452-5400

11,600,30624,090,795 Shares

TRANSGENOMIC, INC.

COMMON STOCK

PROSPECTUS

, 20042006

PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

Item 14. Other Expenses of Issuance and Distribution.

The following table showsindicates the estimated expenses to be incurred in connection with the issuanceoffering described in this Registration Statement, other than the underwriting discounts and distributioncommissions, all of which will be paid by the common stock being registered:Company. All amounts are estimates, other than the SEC registration fee and the NASD filing fee.

Item 15. Indemnification of Directors and Officers.Section 145 of the Delaware General Corporation Law authorizes a court to award, or a corporation to grant, indemnity to directors and officers in terms sufficiently broad to permit such indemnification under certain circumstances for liabilities (including reimbursement of expenses incurred) arising under the Securities Act of 1933.

As permitted by the Delaware General Corporation Law, the Registrant’s FirstThird Restated Certificate of Incorporation eliminates the personal liability of its directors for monetary damages for breach of fiduciary duty as a director, except for liability (1) for any breach of the director’s duty of loyalty to the Registrant or its stockholders, (2) for acts or omissions not in good faith or that involve intentional misconduct or a knowing violation of law, (3) under Section 174 of the Delaware General Corporation Law (regarding unlawful dividends and stock purchases) or (4) for any transaction from which the director derived an improper personal benefit. If the Delaware General Corporation Law is amended to authorize further elimination or limiting of directors’ personal liability, then the FirstThird Amended and Restated Certificate provides that the personal liability of directors will be eliminated or limited to the fullest extent provided under the Delaware General Corporation Law.

As permitted by the Delaware General Corporation Law, the Registrant’s FirstThird Amended and Restated Certificate of Incorporation and its Bylaws provide that (1) the Registrant is required to indemnify its directors and officers to the fullest extent permitted by the Delaware General Corporation Law, subject to certain very limited exceptions, (2) the Registrant may indemnify its other employees and agents as set forth in the Delaware General Corporation Law, (3) the Registrant is required to advance expenses, as incurred, to its directors and executive officers in connection with a legal proceeding to the fullest extent permitted by the Delaware General Corporation Law, subject to certain conditions and (4) the rights conferred by the FirstThird Amended and Restated Certificate of Incorporation and Bylaws are not exclusive.

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The Delaware General Corporation Law authorizes a corporation to indemnify its directors and officers provided that the corporation shall not eliminate or limit the liability of a director as follows:

(a) for any action brought by or in the right of a corporation where the director or officer is adjudged to be liable to the corporation, except where a court determines the director or officer is entitled to indemnity;

(b) for acts or omissions not in good faith or which involve conduct that the director or officer believes is not in the best interests of the corporation;

(c) for knowing violations of the law;

(d) for any transaction from which the directors derived an improper personal benefit; and

The Delaware General Corporation Law requires a corporation to indemnify a director or officer to the extent that the director or officer has been successful, on the merits or otherwise, in defense of any action, suit or proceeding for which indemnification is lawful.

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The RegistrantCompany maintains a director and officer insurance policy which insures the directors and officers of the RegistrantCompany against damages, judgments, settlements and costs incurred by reason of certain wrongful acts committed by such persons in their capacities as directors and officers.

Item 16. Exhibits.

Item 17. Undertakings.II-2

We undertake:

(1) To file, during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

(i) to include any prospectus required by section 10(a)(3) of the Securities Act of 1933;

(ii) to reflect in the prospectus any facts or events arising after the effective date of this registration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forth in this registration statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of a prospectus filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than a 20% change in the maximum aggregate offering price set forth in the “Calculation of Registration Fee” in this registration statement;

(iii) to include any material information with respect to the plan of distribution not previously disclosed in this registration statement or any material change to such information in this registration statementstatement; provided, however,, that the undertakings set forth in paragraphs (i) and (ii) above do not apply if the information required to be included in a post-effective amendment by those paragraphs is contained in periodic reports filed with or furnished to the Commission by the Registrant pursuant to section 13 or section 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in this registration statement.

(2) That, for the purpose of determining any liability under the Securities Act of 1933, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(3) To remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.

(4) That, for purposes of determining any liability under the Securities Act of 1933, each filing of the Registrant’s annual report pursuant to section 13(a) or section 15(d) of the Securities Exchange Act of 1934 that is incorporated by reference in this registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

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(5) Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling persons of the Registrant pursuant to the foregoing provisions, or otherwise, the Registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as expressed in the Securities Act of 1933 and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the Registrant of expenses incurred or paid by a director, officer or controlling person of the Registrant in the successful defense of any action, suit or proceeding) is asserted against the Registrant by such director, officer or controlling person in connection with the securities being

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registered, the Registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act of 1933 and will be governed by the final adjudication of such issue.

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SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-3 and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in Omaha, Nebraska, on the 13^th day of September, 2004.July 14, 2006.

POWER OF ATTORNEY

Each personKNOW ALL MEN BY THESE PRESENTS, that the undersigned, whose signature appearssignatures appear below, hereby authorizes Collin J. D’Silvaconstitute and appoint Michael Summers as their true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for them and in their name, place and stead, in any and all capacities, to sign on his or her behalf, individuallyany and in each capacity stated below, any amendment, includingall amendments (including post-effective amendmentsamendments) to this Registration Statement,registration statement, and to file the same, with all exhibits thereto, and allother documents in connection therewith, with the Securities and Exchange Commission.

Commission, granting unto said attorney-in-fact and agent full power and authority to do and perform each and every act and thing requisite and necessary to be done, as full and to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorney-in-fact and agent, or his substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has been signed below by the following persons in the capacities and on the dates indicated.

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EXHIBIT INDEX