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                                                                    EXHIBIT 99.3
 
                              MEDAPHIS CORPORATION
               INSTRUCTION TO REGISTERED HOLDER AND/OR DEPOSITORY
                TRUST COMPANY PARTICIPANT FROM BENEFICIAL OWNER
                                      FOR
                             OFFER TO EXCHANGE ITS
                     SERIES B 9 1/2% SENIOR NOTES DUE 2005
                       FOR ANY AND ALL OF ITS OUTSTANDING
                     SERIES A 9 1/2% SENIOR NOTES DUE 2005
  THE EXCHANGE OFFER AND WITHDRAWAL RIGHTS WILL EXPIRE AT 5:00 P.M., NEW YORK
  CITY TIME, ON          , 1998, UNLESS THE OFFER IS EXTENDED. TENDERS MAY BE
   WITHDRAWN PRIOR TO 5:00 P.M., NEW YORK CITY TIME, ON THE EXPIRATION DATE.
 
To Registered Holder and/or Depository Trust Company Participant:
 
     The undersigned hereby acknowledges receipt of the Prospectus dated
       , 1998 (the "Prospectus") of Medaphis Corporation, a Delaware corporation
(the "Company"), and the accompanying Letter of Transmittal (the "Letter of
Transmittal"), that together constitute the Company's offer (the "Exchange
Offer") to exchange its Series B 9 1/2% Senior Notes Due 2005 (the "New Notes")
for all of its outstanding Series A 9 1/2% Senior Notes Due 2005 (the "Old
Notes"). Capitalized terms used but not defined herein have the meanings
ascribed to them in the Prospectus.
 
     This will instruct you, the registered holder and/or Depository Trust
Company Participant, as to the action to be taken by you relating to the
Exchange Offer with respect to the Old Notes held by you for the account of the
undersigned.
 
     The aggregate face amount of the Old Notes held by you for the account of
the undersigned is (FILL IN AMOUNT):
 
          $          of the 9 1/2% Senior Notes Due 2005.
 
     With respect to the Exchange Offer, the undersigned hereby instructs you
(CHECK APPROPRIATE BOX):
 
        [ ] To TENDER the following Old Notes held by you for the account of the
            undersigned (INSERT PRINCIPAL AMOUNT OF ORIGINAL NOTES TO BE
            TENDERED (IF LESS THAN ALL): $
 
        [ ] NOT to TENDER any Old Notes held by you for the account of the
            undersigned.
 
     If the undersigned instructs you to tender the Old Notes held by you for
the account of the undersigned, it is understood that you are authorized to
make, on behalf of the undersigned (and the undersigned, by its signature below,
hereby makes to you), the representation and warranties contained in the Letter
of Transmittal that are to be made with respect to the undersigned as a
beneficial owner, including but not limited to the representations, that (i) the
undersigned is not an "affiliate" of the Company, (ii) any New Notes to be
received by the undersigned are being acquired in the ordinary course of its
business, (iii) the undersigned has no arrangement or understanding with any
person to participate in a distribution (within the meaning of the Securities
Act) of New Notes to be received in the Exchange Offer, and (iv) if the
undersigned is not a broker-dealer, the undersigned is not engaged in, and does
not intend to engage in, a distribution (within the meaning of the Securities
Act) of such New Notes. The Company may require the undersigned, as a condition
to the undersigned's eligibility to participate in the Exchange Offer, to
furnish to the Company (or an agent thereof) in writing information as to the
number of "beneficial owners" within the meaning of Rule 13d-3 under the
Exchange Act on behalf of whom the undersigned holds the Old Notes to be
exchanged in the Exchange Offer. By tendering Old Notes pursuant to the Exchange
Offer, a holder of Old
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Notes which is a broker-dealer represents and agrees, consistent with certain
interpretive letters issued by the staff of the Division of Corporation Finance
of the Securities and Exchange Commission to third parties, that such Old Notes
were acquired by such broker-dealer for its own account as a result of
market-making activities or other trading activities, and it will deliver a
Prospectus (as amended or supplemented from time to time) meeting the
requirements of the Securities Act in connection with any resale of such New
Notes (provided that, by so acknowledging and by delivering a Prospectus, such
broker-dealer will not be deemed to admit that it is an "underwriter" within the
meaning of the Securities Act).
 
                                   SIGN HERE
 
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                          Name of beneficial owner(s)
 
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                                  Signature(s)
 
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                             Name(s) (please print)
 
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                                   (Address)
 
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                               (Telephone Number)
 
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              (Taxpayer Identification or Social Security Number)
 
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                                      Date