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                                                                     EXHIBIT 3.1


                                   CORRECTED
               AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                                 ILLUMINA, INC.

        Illumina, Inc., a corporation organized and existing under and
by virtue of the General Corporation Law of the State of Delaware (the
"Corporation"), certifies as follows:

        1. The original Amended and Restated Certificate of Incorporation was
filed with the Secretary of State of Delaware on July 7, 2000 (the "Amendment")
and that said Amendment requires correction, as permitted by Section 103 of the
General Corporation Law of the State of Delaware.

        2. The Amendment inaccurately set forth the par value of the authorized
shares of the Corporation in the first paragraph of Article IV and, as
corrected, said Certificate shall read in its entirety as follows:


                AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                                 ILLUMINA, INC.

        Illumina, Inc., a corporation organized and existing under the laws of
the State of Delaware, hereby certifies as follows:

        A. The name of the corporation is Illumina, Inc. The corporation was
originally incorporated under the same name, and the original Certificate of
Incorporation was filed with the Secretary of State of the State of Delaware on
May 16, 2000.

        B. Pursuant to Sections 242 and 245 of the General Corporation Law of
the State of Delaware, this Restated Certificate of Incorporation restates and
amends the provisions of the Certificate of Incorporation of the corporation.

        C. The text of the Certificate of Incorporation is hereby amended and
restated in its entirety to read as follows:

                                    ARTICLE I

        The name of this corporation is Illumina, Inc.

                                   ARTICLE II

        The address of the corporation's registered office in the State of
Delaware is 1209 Orange Street, City of Wilmington, County of New Castle,
Delaware 19801. The name of its registered agent at such address is The
Corporation Trust Company.

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                                   ARTICLE III

        The purpose of the corporation is to engage in any lawful act or
activity for which a corporation may be organized under the General Corporation
Law of Delaware.

                                   ARTICLE IV

        The corporation is authorized to issue two classes of shares of stock to
be designated, respectively, Common Stock, $0.01 par value, and Preferred Stock,
$0.01 par value. The total number of shares that the corporation is authorized
to issue is 130,000,000 shares. The number of shares of Common Stock authorized
is 120,000,000. The number of shares of Preferred authorized is 10,000,000.

        The Preferred Stock may be issued from time to time in one or more
series pursuant to a resolution or resolutions providing for such issue duly
adopted by the board of directors (authority to do so being hereby expressly
vested in the board). The board of directors is further authorized to determine
or alter the rights, preferences, privileges and restrictions granted to or
imposed upon any wholly unissued series of Preferred Stock and to fix the number
of shares of any series of Preferred Stock and the designation of any such
series of Preferred Stock. The board of directors, within the limits and
restrictions stated in any resolution or resolutions of the board of directors
originally fixing the number of shares constituting any series, may increase or
decrease (but not below the number of shares of any such series then
outstanding) the number of shares of any series subsequent to the issue of
shares of that series.

        The authority of the board of directors with respect to each such class
or series shall include, without limitation of the foregoing, the right to
determine and fix:

               (a) the distinctive designation of such class or series and the
number of shares to constitute such class or series;

               (b) the rate at which dividends on the shares of such class or
series shall be declared and paid, or set aside for payment, whether dividends
at the rate so determined shall be cumulative or accruing, and whether the
shares of such class or series shall be entitled to any participating or other
dividends in addition to dividends at the rate so determined, and if so, on what
terms;

               (c) the right or obligation, if any, of the corporation to redeem
shares of the particular class or series of Preferred Stock and, if redeemable,
the price, terms and manner of such redemption;

               (d) the special and relative rights and preferences, if any, and
the amount or amounts per share that the shares of such class or series of
Preferred Stock shall be entitled to receive upon any voluntary or involuntary
liquidation, dissolution or winding up of the corporation;

               (e) the terms and conditions, if any, upon which shares of such
class or series shall be convertible into, or exchangeable for, shares of
capital stock of any other class or series,


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including the price or prices or the rate or rates of conversion or exchange and
the terms of adjustment, if any;

               (f) the obligation, if any, of the corporation to retire, redeem
or purchase shares of such class or series pursuant to a sinking fund or fund of
a similar nature or otherwise, and the terms and conditions of such obligation;

               (g) voting rights, if any, on the issuance of additional shares
of such class or series or any shares of any other class or series of Preferred
Stock;

               (h) limitations, if any, on the issuance of additional shares of
such class or series or any shares of any other class or series of Preferred
Stock; and

               (i) such other preferences, powers, qualifications, special or
relative rights and privileges thereof as the board of directors of the
corporation, acting in accordance with this Restated Certificate of
Incorporation, may deem advisable and are not inconsistent with law and the
provisions of this Restated Certificate of Incorporation.

                                    ARTICLE V

        The corporation reserves the right to amend, alter, change, or repeal
any provision contained in this Certificate of Incorporation, in the manner now
or hereafter prescribed by statute, and all rights conferred upon the
stockholders herein are granted subject to this right.

                                   ARTICLE VI

        The corporation is to have perpetual existence.

                                   ARTICLE VII

        1. Limitation of Liability. To the fullest extent permitted by the
General Corporation Law of the State of Delaware as the same exists or as may
hereafter be amended, a director of the corporation shall not be personally
liable to the corporation or its stockholders for monetary damages for breach of
fiduciary duty as a director.

        2. Indemnification. The corporation shall indemnify to the fullest
extent permitted by law any person made or threatened to be made a party to an
action or proceeding, whether criminal, civil, administrative or investigative,
by reason of the fact that such person or his or her testator or interstate is
or was a director or officer of the corporation, or any predecessor of the
corporation, or serves or served at any other enterprise as a director, officer
or employee at the request of the corporation or any predecessor to the
corporation and may indemnify to the fullest extent permitted by law any person
made or threatened to be made a party to an action or proceeding, whether
criminal, civil, administrative or investigative, by reason of the fact that
such person or his or her testator or intestate is or was an employee of the
corporation, or any predecessor of the corporation, or serves or served at any
other enterprise as a director, officer or employee at the request of the
corporation or any predecessor to the corporation.



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        3. Amendments. Neither any amendment nor repeal of this Article VII, nor
the adoption of any provision of the corporation's Certificate of Incorporation
inconsistent with this Article VII, shall eliminate or reduce the effect of this
Article VII, in respect of any matter occurring, or any action or proceeding
accruing or arising or that, but for this Article VII, would accrue or arise,
prior to such amendment, repeal, or adoption of an inconsistent provision.

                                  ARTICLE VIII

        In the event any shares of Preferred Stock shall be redeemed or
converted pursuant to the terms hereof, the shares so converted or redeemed
shall not revert to the status of authorized but unissued shares, but instead
shall be canceled and shall not be re-issuable by the corporation.

                                   ARTICLE IX

        Holders of stock of any class or series of the corporation shall not be
entitled to cumulate their votes for the election of directors or any other
matter submitted to a vote of the stockholders, unless such cumulative voting is
required pursuant to Sections 214 of the Delaware General Corporation Law, in
which event each such holder shall be entitled to as many votes as shall equal
the number of votes which (except for this provision as to cumulative voting)
such holder would be entitled to cast for the election of directors with respect
to his shares of stock multiplied by the number of directors to be elected by
him, and the holder may cast all of such votes for a single director or may
distribute them among the number of directors to be voted for, or for any two or
more of them as such holder may see fit, so long as the name of the candidate
for director shall have been placed in nomination prior to the voting and the
stockholder, or any other holder of the same class or series of stock, has given
notice at the meeting prior to the voting of the intention to cumulate votes.

        1. Number of Directors. The number of directors which constitutes the
whole Board of Directors of the corporation shall be designated in the Amended
and Restated Bylaws of the corporation. The directors shall be divided into
three classes with the term of office of the first class (Class I ) to expire at
the annual meeting of the stockholders held in 2001; the term of office of the
second class (Class II) to expire at the annual meeting of stockholders held in
2002; the term of office of the third class (Class III) to expire at the annual
meeting of stockholders held in 2003; and thereafter for each such term to
expire at each third succeeding annual meeting of stockholders after such
election.

        2. Election of Directors. Elections of directors need not be by written
ballot unless the Amended and Restated Bylaws of the corporation shall so
provide.

                                    ARTICLE X

        In furtherance and not in limitation of the powers conferred by statute,
the Board of Directors is expressly authorized to make, alter, amend or repeal
the Amended and Restated Bylaws of the corporation.



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                                   ARTICLE XI

        No action shall be taken by the stockholders of the corporation except
at an annual or special meeting of the stockholders called in accordance with
the Amended and Restated Bylaws, no special meetings of the stockholders shall
be called by stockholders without approval of the Board of Directors, and no
action, including the removal of directors without cause shall be taken by
stockholders by written consent. The affirmative vote of sixty-six and
two-thirds percent (66 2/3%) of the then outstanding voting securities of the
corporation, voting together as a single class, shall be required for the
amendment, repeal or modification of the provisions of Article IX, Article X or
Article XII of this Amended and Restated Certificate of Incorporation or
Sections 2.3 (Special Meeting), 2.4 (Notice of Stockholders' Meeting), 2.4
(Advanced Notice of Stockholder Nominees and Stockholder Business), 2.8
(Voting), or 2.10 (Stockholder Action by Written Consent Without a Meeting), or
3.2 (Number of Directors) of the corporation's Amended and Restated Bylaws.

                                   ARTICLE XII

        Meetings of stockholders may be held within or without the State of
Delaware, as the Amended and Restated Bylaws may provide. The books of the
corporation may be kept (subject to any provision contained in the statutes)
outside of the State of Delaware at such place or places as may be designated
from time to time by the Board of Directors or in the Amended and Restated
Bylaws of the corporation.

                                  ARTICLE XIII

        This Amended and Restated Certificate of Incorporation shall be
effective as of the date of the closing of the Corporation's initial public
offering.


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        IN WITNESS WHEREOF, Illumina, Inc. has caused this certificate
to be signed by Jay T. Flatley, its President and Chief Executive
Officer, this 21st day of March, 2001.



                                               /s/ Jay T. Flatley
                                               ---------------------------------
                                               Jay T. Flatley,
                                               President and Chief
                                               Executive Officer