UNITED STATES SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
                                    FORM 10-K/A
                          Amendment No. 1 to Form 10-K
(Mark One)
  X ANNUAL REPORT  PURSUANT TO SECTION 13 OR 15(d) OF THE  SECURITIES  EXCHANGE
    ACT OF 1934 For the fiscal year ended June 30, 1998
                                       OR
   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE 
    ACT OF 1934

Commission file number 0-15609

                          Agouron Pharmaceuticals, Inc.
             (Exact name of registrant as specified in its charter)


          California                                      33-0061928
(State or other jurisdiction of              (I.R.S. EmployerIdentification No.)
 incorporation or organization)

10350 North Torrey Pines Road, La Jolla, California                92037-1020
(Address of principal executive offices)                           (Zip Code)

Registrant's telephone number, including area code:              (619) 622-3000

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

Securities registered pursuant to Section 12(g) of the Act:

                         Common Stock, without par value
                                (Title of class)

     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  Exchange  Act of
1934  during  the  preceding  12 months  (or for such  shorter  period  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. [ ]

     On July 28, 1998,  the  aggregate  market value of the common stock held by
nonaffiliates  totaled  approximately  $724,738,000  based on the closing  stock
price as reported by The Nasdaq Stock Market.

     On July 28,  1998,  there were  approximately  31,097,000  shares of common
stock, without par value, of the registrant issued and outstanding.

                       DOCUMENTS INCORPORATED BY REFERENCE

         The registrant's  definitive proxy statement to be prepared pursuant to
Regulation  14A and filed in  connection  with  solicitation  of proxies for its
Annual Meeting of Stockholders,  to be held on October 28, 1998, is incorporated
by reference into Part III of this Form 10-K.

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                                     PART IV


Item 14.      EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K

 (a)          List of documents filed as part of this report:

              (1)     Financial Statements and Supplementary Data
                      Reference is made to the Index to Financial Statements and
                      Schedules  under  Item 8 in Part II  hereof,  where  these
                      documents are listed.
              (2)     Exhibits - see (c) below

 (b)          Reports on Form 8-K

     No reports on Form 8-K were filed during the fourth quarter of fiscal 1998.

(c)           Exhibits

         Exhibit
         Number                             Exhibit
         --------     ----------------------------------------------------------

           2.1(a)     Agreement and Plan of Reorganization dated as of April 28,
                      1997,  between  Agouron  Pharmaceuticals,   Inc.,  Agouron
                      Acquisition Corporation and Alanex Corporation.
           3.1(b)     Restated Articles of Incorporation (December 10, 1992).
           3.2(c)     Amended and Restated Bylaws (Restated June 17, 1991).
           4.1(d)     Rights  Agreement  dated  November 7, 1996,  as amended on
                      November  27,  1996,  between the Company and Chase Mellon
                      Shareholder  Services.  L.L.C., which includes, as Exhibit
                      A,  the  Certificate  of  Determination,  Preferences  and
                      Rights of Series B Participating  Preferred Stock as filed
                      with the  California  Secretary  of State on November  20,
                      1996.
         10.01(h)     1990 Stock Option Plan (Restated November 2, 1995).
         10.02(k)     Form of 1990 Incentive Stock Option Agreement.
         10.03(k)     Form of 1990 Non-Statutory Stock Option Agreement for 
                      Employees/Officers/Directors.
         10.04(k)     Form of 1990 Non-Statutory Stock Option Agreement for 
                      Consultants.
         10.05(c)     1985 Stock Option Plan (Last Amended August 14, 1991).
         10.06(e)     Agouron Pharmaceuticals, Inc. 401(k) Plan
                      (Amended August 1992).
         10.07(b)     Agouron Pharmaceuticals, Inc. Employee Stock Purchase Plan
                      (October 15, 1992).
         10.08(b)     Agouron Pharmaceuticals, Inc. Flexible Benefits Plan 
                      (December 10, 1992).
         10.09(f)     Agreement  Two  dated  February  28,  1994  between  Japan
                      Tobacco  Inc.  and  the  Company.
                      (Portions of the agreement receive confidential  treatment
                      pursuant to an application  filed April 25, 1994; File No.
                      0-15609).

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         Exhibit
         Number                             Exhibit
         --------     ----------------------------------------------------------

         10.10(g)     Development  and License  Agreement dated December 1, 1994
                      between  Japan  Tobacco Inc. and the Company  (Portions of
                      the agreement receive  confidential  treatment pursuant to
                      an application dated January 31, 1995).
         10.11(h)     First  Amendment  to  Development  and  License  Agreement
                      effective  December 1, 1994 between Japan Tobacco Inc. and
                      the Company.  (Confidential  treatment has been  requested
                      for portions of this agreement  pursuant to an application
                      dated January 31, 1996. The underlying agreement was filed
                      as  Exhibit  10.54  on  Form  10-Q  for the  period  ended
                      December  31,   1994,   and   portions   thereof   receive
                      confidential   treatment  pursuant  to  an  order  of  the
                      Securities and Exchange Commission dated June 28, 1995.)
         10.12(i)     Amendment effective January 1, 1996 to the Agouron
                      Pharmaceuticals, Inc. 401(k) Plan.
         10.13(j)     1996 Stock Option Plan.
         10.14(j)     Form of 1996 Incentive Stock Option Agreement.
         10.15(j)     Form  of  1996  Non-Statutory   Stock  Option  Agreement
                      for Employees/Officers/Directors.
         10.16(j)     Form  of  1996  Stock  Option
                      Agreement for Consultants  10.17(l) Second Amendment to 
                      Development and License Agreement effective January 17, 
                      1997 between Japan   Tobacco  Inc.   and  the  Company
                      (Confidential treatment   has  been   requested  for  
                      portions  of  this agreement  pursuant  to an  application
                      dated  August 21, 1997, as separately filed with the
                      Securities and Exchange Commission.  The underlying 
                      agreement was filed as Exhibit 10.54 on Form 10-Q for the
                      period ended December 31, 1994, and  portions  thereof  
                      receive   confidential   treatment pursuant  to an  orde
                      of  the  Securities  and  Exchange Commission dated
                      June 28, 1995.)
         10.18(l)     Third  Amendment  to  Development  and  License  Agreement
                      effective  December 1, 1996 between Japan Tobacco Inc. and
                      the Company.  (Confidential  treatment has been  requested
                      for portions of this agreement  pursuant to an application
                      dated  August  21,  1997,  as  separately  filed  with the
                      Securities   and  Exchange   Commission.   The  underlying
                      agreement  was filed as Exhibit 10.54 on Form 10-Q for the
                      period  ended  December 31,  1994,  and  portions  thereof
                      receive confidential treatment pursuant to an order of the
                      Securities and Exchange Commission dated June 28, 1995.)
         10.19(l)     VIRACEPT License  Agreement  between the Company and Japan
                      Tobacco Inc. and F.  Hoffmann-La  Roche Ltd dated June 30,
                      1997.  (Confidential  treatment  has  been  requested  for
                      portions  of this  agreement  pursuant  to an  application
                      dated  August  21,  1997,  as  separately  filed  with the
                      Securities and Exchange Commission.)
         10.20(m)     Form of 1998 Employee Stock Option Plan.
         10.21(m)     Form of 1998 Employee Non-Statutory Stock Option
                      Agreement.


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         Exhibit
         Number                             Exhibit
         --------     ----------------------------------------------------------

         10.22        License and Supply Agreement between the Company and Japan
                      Energy   Corporation   effective  as  of  June  30,  1998.
                      (Confidential treatment has been requested for portions of
                      this agreement  pursuant to an application dated August 4,
                      1998, as separately filed with the Securities and Exchange
                      Commission.)
         10.23        Common  Stock  Purchase   Agreement   between  The  Immune
                      Response  Corporation and the Company dated June 11, 1998.
                      (Confidential treatment has been requested for portions of
                      this agreement  pursuant to an application dated August 4,
                      1998, as separately filed with the Securities and Exchange
                      Commission.)
         10.24        Amendment to the VIRACEPT  License  Agreement  between the
                      Company and Japan  Tobacco Inc. and F.  Hoffmann-La  Roche
                      Ltd as of May 1, 1998.  (Confidential  treatment  has been
                      requested  for portions of this  agreement  pursuant to an
                      application dated August 4, 1998, as separately filed with
                      the Securities and Exchange Commission.)
         21/#/        Subsidiaries of Agouron Pharmaceuticals, Inc.
         23.1/#/      Consent of Independent Accountants.
         27/#/        Financial  Data  Schedule.  (Exhibit 27 is  submitted  as
                      an exhibit  only in the  electronic format of this  Annual
                      Report on Form 10-K submitted to the Securities and
                      Exchange Commission.)
         99/#/        Important Factors Regarding Forward-Looking Statements.

     #  Previously filed

     (a) Incorporated by Reference to Form 8-K filed on May 23, 1997.
     (b)  Incorporated  by  Reference  to Form 10-Q filed for the quarter  ended
     December 31, 1992. (c) Incorporated by Reference to Form 10-K filed for the
     year ended June 30, 1991.  (d)  Incorporated  by  Reference  for Form 8-K/A
     filed on December  20,  1996.  (e)  Incorporated  by Reference to Form 10-K
     filed for the year ended June 30, 1992.  (f)  Incorporated  by Reference to
     Form 10-Q/A filed for the quarter ended March 31, 1994. (g) Incorporated by
     Reference to Form 10-Q filed for the quarter ended  December 31, 1994.  (h)
     Incorporated by Reference to Form 10-Q filed for the quarter ended December
     31, 1995. (i)  Incorporated by Reference to Form 10-Q filed for the quarter
     ended March 31, 1996.  (j)  Incorporated  by Reference to Form S-8 filed on
     November  26,  1996.  (k)  Incorporated  by  Reference to Form 10-Q for the
     quarter ended December 31, 1996. (l) Incorporated by Reference to Form 10-K
     for the year ended June 30, 1997. (m) Incorporated by Reference to Form S-8
     filed on February 19, 1998.

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                                   Signatures

     Pursuant  to the  requirements  of  Section  13 or 15(d) 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.
                                   AGOURON PHARMACEUTICALS, INC.

August 7, 1998                     By:  /s/ Steven S. Cowell
                                   ---------------------------------
                                   Steven S. Cowell
                                   Corporate Vice President
                                   Chief Financial Officer


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