<PAGE>   1
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                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

   
                                    FORM 10-K/A
    

(X)  ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934

                  For the fiscal year ended SEPTEMBER 30, 1997

( )  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
     EXCHANGE ACT OF 1934 

              For the transition period from ________ to ________

                           Commission File No. 0-18734

                              LIDAK PHARMACEUTICALS
             (Exact name of registrant as specified in its charter)

                 CALIFORNIA                           33-0314804
       (State or other jurisdiction of     (IRS Employer Identification No).
        incorporation or organization)

         11077 N. TORREY PINES ROAD
            LA JOLLA, CALIFORNIA                        92037
     (Address of principal executive office)         (Zip Code)

                                 (619) 558-0364
              (Registrant's telephone number, including area code)

        Securities registered pursuant to Section 12(b) of the Act: None

            Securities registered pursuant to Section (g) of the Act:

                       Class A Common Stock, no par value

Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities and Exchange Act of 1934
during the preceding 12 months (or for such shorter periods that the registrant
was required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days. YES [X] NO

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this form 10-K or any amendment to this
form 10-K. [X]

The aggregate market value of the Registrant's voting stock, held by
non-affiliates, computed by reference to the average of the closing bid and
asked prices of the Class A Common Stock as reported by NASDAQ on December 29,
1997: $90,771,229.

The number of shares of Common Stock of the Registrant issued and outstanding as
of December 29, 1997:

     Class A common stock, no par value                  38,742,511
     Class B common stock, no par value                     283,000

                       DOCUMENTS INCORPORATED BY REFERENCE
Registrant's definitive Proxy Statement which will be filed with the Securities
and Exchange Commission on or before January 28, 1998 in connection with
Registrant's annual meeting of stockholders to be held on March 14, 1998 is
incorporated by reference into Part III of this Report.

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<PAGE>   2
                                   SIGNATURES

   
     Pursuant to the requirements of the Securities Exchange Act of 1934, the
Registrant has duly caused this report to be signed on its behalf by the
undersigned, thereunto duly authorized.

Date: January 8, 1998
                                        LIDAK PHARMACEUTICALS

                                        By: /s/David H. Katz
                                           --------------------------------
                                           David H. Katz, M.D.
                                           President and Chief Executive Officer

     Pursuant to the requirements of the Securities Exchange Act of 1934, this
report has been signed below by the following persons on behalf of the
Registrant and in the capacities and on the date indicated.

<TABLE>
<CAPTION>
Signature                                        Title                                  Date
---------                                        -----                                  ----
<S>                                     <C>                                             <C> 
/s/David H. Katz                        President and Chief                             January 8, 1998
------------------------------------    Executive Officer
David H. Katz, M.D.                     (Principal Executive Officer)
                                    

/s/Jeffery B. Weinress                  Vice President and Chief                        January 8, 1998
------------------------------------    Financial Officer
Jeffery B. Weinress                     (Principal Financial and Accounting Officer)
                                    


/s/Daniel J. Paracka                    Chairman of the Board                           January 8, 1998
------------------------------------
Daniel J. Paracka


/s/Helmer P.K. Agersborg, Jr.           Director                                        January 8, 1998
------------------------------------
Helmer P.K. Agersborg, Jr., Ph.D.


/s/William N. Jenkins                   Director                                        January 8, 1998
------------------------------------
William N. Jenkins


/s/Kenneth E. Olson                     Director                                        January 8, 1998
------------------------------------
Kenneth E. Olson


/s/Stuart A. Samuels                    Director                                        January 8, 1998
------------------------------------
Stuart A. Samuels


/s/Sidney N. Towle, Jr.                 Director                                        January 8, 1998
------------------------------------
Sidney N. Towle, Jr.
</TABLE>
    



                                       35
<PAGE>   3




LIDAK PHARMACEUTICALS
(A DEVELOPMENT STAGE ENTERPRISE)

STATEMENTS OF CASH FLOWS
FOR THE YEARS ENDED SEPTEMBER 30, 1995, 1996 AND 1997, AND THE PERIOD
AUGUST 31, 1988 (INCEPTION) TO SEPTEMBER 30, 1997
--------------------------------------------------------------------------------

   
<TABLE>
<CAPTION>

                                                                                                             AUGUST 31, 1988
                                                                YEARS ENDED SEPTEMBER 30,                    (INCEPTION) TO
                                                   ----------------------------------------------------       SEPTEMBER 30,
                                                        1995              1996                 1997                1997
<S>                                                <C>                 <C>                 <C>                 <C>
OPERATING ACTIVITIES:
  Net Loss                                         $(10,173,001)       $ (6,130,241)       $(11,109,242)       $(45,405,440)
  Adjustments to reconcile net loss to
    net cash used for operating activities:
    Depreciation and amortization                        84,867             292,943             136,820             733,703
    Non-cash interest expense                                             2,771,030           1,470,434           4,241,464
    Technology license fee                                                                                        3,545,713
    Compensation paid with common stock
      and stock options                                 129,792                                  86,167             661,792
    Compensation forgiven by stockholder                                                                             66,923
    Imputed interest on technology
      license fee                                                                                                    82,613
    Changes in assets and liabilities:
      Interest receivable                               (16,913)           (283,652)            228,875            (109,528)
      Prepaid and other                                 (77,111)           (908,513)            823,923            (267,786)
      Patent costs                                     (113,535)           (163,822)            (54,445)           (675,869)
      Organizational costs                                                                                          (20,242)
      Accounts payable                                  812,040            (190,813)           (563,501)            765,917
      Accrued compensation and payroll taxes             44,436              37,560              19,048             225,493
      Due to MBI                                          1,064               5,483               4,888              26,698
      Deferred revenue                                                      500,000            (500,000)
                                                     ----------          ----------          ----------         ------------
        Net cash used for operating
          activities:                                (9,308,361)         (4,070,025)         (9,457,033)        (36,128,549)
                                                     ----------          ----------          ----------         ------------

INVESTING ACTIVITIES:
  Short-term investments                              7,115,856          (1,235,350)          7,026,502
  Capital expenditures                                  (92,871)           (122,425)            (50,059)           (592,699)
  Note receivable - employee                            138,649
                                                     ----------          ----------          ----------         ------------

        Net cash provided by (used for)
          investing activities                        7,161,634          (1,357,775)          6,976,443            (592,699)
                                                     ----------          ----------          ----------         ------------

FINANCING ACTIVITIES:
  Proceeds from issuance of common
      and preferred stock                             1,922,157           1,885,579             531,192          39,209,463
  Proceeds from issuance of convertible
      notes payable                                                      13,500,000           6,000,000          19,500,000
</TABLE>

See notes to financial statements.                                (Continued)-1
    



                                      F-10


<PAGE>   4

LIDAK PHARMACEUTICALS
(A DEVELOPMENT STAGE ENTERPRISE)

STATEMENTS OF CASH FLOWS
FOR THE YEARS ENDED SEPTEMBER 30, 1995, 1996 AND 1997, AND THE PERIOD
AUGUST 31, 1988 (INCEPTION) TO SEPTEMBER 30, 1997
--------------------------------------------------------------------------------

   
<TABLE>
<CAPTION>
                                                                                                            AUGUST 31, 1988
                                                             YEARS ENDED SEPTEMBER 30,                      (INCEPTION) TO
                                                  --------------------------------------------------         SEPTEMBER 30,
                                                       1995              1996              1997                  1997     
<S>                                               <C>                 <C>                 <C>                <C>        
FINANCING ACTIVITIES (Continued):
  Debt issue costs                                                      (771,351)            (296,059)         (1,067,410)
  Repayment of convertible notes payable                                                   (2,673,217)         (2,673,217)
  Stock issue costs                                  (26,743)            (83,495)                              (2,913,703)
  Advances for purchase of common stock                                                                           125,000
  Collection of notes receivable for
    common stock                                                                                                   14,525
  Proceeds from stockholder loans                                                                                 322,788
  Repayment of stockholder loans                                                                                 (322,788)
  Proceeds from issuance of
    subordinated notes payable -
      net of issue costs                                                                                          538,750
  Repayment of subordinated notes payable                                                                        (625,000)
  Payment on technology license fee                                                                              (958,326)
                                                ------------        ------------       ------------         -------------
      Net cash provided by financing
         activities                                1,895,414          14,530,733           3,561,916           51,150,082
                                                ------------        ------------       ------------         -------------

NET INCREASE (DECREASE)
  IN CASH AND CASH EQUIVALENTS                      (251,313)          9,102,933           1,081,326           14,428,834

CASH AND CASH EQUIVALENTS
  AT BEGINNING OF PERIOD                           4,495,888           4,244,575          13,347,508
                                                ------------        ------------        ------------         -------------

CASH AND CASH EQUIVALENTS
  AT END OF PERIOD                              $  4,244,575        $ 13,347,508        $ 14,428,834        $  14,428,834
                                                ============        ============       =============        =============

SUPPLEMENTAL DISCLOSURES
  OF CASH FLOW INFORMATION:
    Interest paid                                                   $     77,433        $    784,224        $     993,763
                                                                    ============       =============        =============
</TABLE>
    



See notes to financial statements.                                (Concluded) -2



                                      F-11