UNITED STATES
                    SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C. 20549

                                 FORM 10-Q


         (X)    QUARTERLY REPORT UNDER SECTION 13 OR 15(d) OF THE 
                      SECURITIES EXCHANGE ACT OF 1934

                  For the quarterly period ended March 31, 1996

                                     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. employer identification no.)
   incorporation or organization)


       10350 NORTH TORREY PINES ROAD, LA JOLLA, CALIFORNIA  92037-1020
            (Address and zip code of principal executive offices)

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

                                   NONE
             (Former name, former address and former fiscal year,
                       if changed since last report.)

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 the number of shares outstanding of each of the issuer's classes of 
common stock, as of the latest practicable date:  Approximately 10,627,000 
shares of the Company's Common Stock, no par value, were outstanding as of 
April 19, 1996. 







                        AGOURON PHARMACEUTICALS, INC.

                                   INDEX

                                                            Page No.
Part I.     Financial Information

Item 1.     Financial Statements

            Balance Sheet -                                     3
                 March 31, 1996 and June 30, 1995     

            Statement of Operations - Three and Nine            4
                 Months Ended March 31, 1996 and 1995

            Statement of Cash Flows -                           5
                 Nine Months Ended March 31, 1996 and 1995

            Notes to Financial Statements                       6

Item 2.     Management's Discussion and Analysis of Financial   7
                 Condition and Results of Operations

Part II.    Other Information          

Item 1.     Legal Proceedings                                   9

Item 2.     Changes in Securities                               9

Item 3.     Defaults Upon Senior Securities                     9

Item 4.     Submission of Matters to a Vote of Security Holders 9

Item 5.     Other Information                                   9

Item 6.     Exhibits and Reports on Form 8-K                    9

            Signature                                          10
          



















PART I.  FINANCIAL INFORMATION

Item 1.  Financial Statements

                        AGOURON PHARMACEUTICALS, INC.
                               BALANCE SHEET
                           (Dollars in thousands)

                                                  March 31,     June 30,
                                                      1996         1995
                                                (unaudited)
ASSETS

Current assets:
     Cash and cash equivalents                   $  14,547     $   4,358
     Short-term investments                         90,109        15,886
     Accounts receivable                               350           344
     Other current assets                            2,242           871
                                                 _________     _________
     Total current assets                          107,248        21,459

Property and equipment, net of accumulated
     depreciation and amortization of 
     $13,035 and $11,344                             5,943         5,638
                                                 _________     _________

                                                 $ 113,191     $  27,097
                                                 =========     =========
LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                            $   8,752     $   5,426
     Accrued liabilities                             1,075           683
     Deferred revenue                               24,763         5,745
     Current portion of long-term debt                 542           768
                                                 _________     _________
     Total current liabilities                      35,132        12,622
                                                 _________     _________
Long-term liabilities:
     Long-term debt, less current portion              606           580
     Accrued rent                                    1,257         1,304
                                                 _________     _________
     Total long-term liabilities                     1,863         1,884
                                                 _________     _________
Stockholders' equity:
     Common stock, no par value, 75,000,000 
        shares authorized, 10,622,800 and 
        7,359,282 shares issued and outstanding    157,379        76,113
     Accumulated deficit                           (81,183)      (63,522)
                                                 _________     _________
     Total stockholders' equity                     76,196        12,591 
                                                 _________     _________

                                                 $ 113,191     $  27,097
                                                 =========     =========

               See accompanying notes to financial statements.

                          AGOURON PHARMACEUTICALS, INC.
                            STATEMENT OF OPERATIONS
                                  (Unaudited)
                (Dollars in thousands, except per share amounts)



                                   Three Months Ended     Nine Months Ended
                                         March 31,             March 31,

                                      1996       1995       1996       1995

Revenues:
     Contract                    $   6,910  $   6,949  $  27,465  $  19,285
     Interest                        1,526        336      3,520        978
                                 _________  _________  _________  _________

                                     8,436      7,285     30,985     20,263
                                 _________  _________  _________  _________

Costs and expenses:
     Research and development       17,064      9,330     43,780    24,352
     General and administrative      2,338      1,162      4,679     3,027
     Interest                           40         63        187       169
                                 _________  _________  _________  _________

                                    19,442     10,555     48,646    27,548
                                 _________  _________  _________  _________

Net loss                         $ (11,006) $  (3,270) $ (17,661) $ (7,285)
                                 ========== =========  =========  =========

Net loss per common share        $   (1.04) $    (.45) $   (1.84) $  (1.00)
                                 ========== =========  =========  =========


Shares used in computing net 
     loss per common share       10,571,000 7,300,000  9,574,000  7,286,000
                                 ========== =========  =========  =========













                See accompanying notes to financial statements.





                         AGOURON PHARMACEUTICALS, INC.
                            STATEMENT OF CASH FLOWS
                                  (Unaudited)
                             (Dollars in thousands)


                                                      Nine Months Ended 
                                                          March 31,
                                                      1996          1995
Cash flows from operating activities:
     Cash received from contracts                $  46,477     $  21,018
     Cash paid to suppliers, employees
           and service providers                   (44,419)      (22,405)
     Interest received                               3,520           978
     Interest paid                                    (187)         (169)
                                                 _________     _________ 
     Net cash provided (used) by operating 
           activities                                5,391          (578)
                                                 _________     _________ 
Cash flows from investing activities:
     Net (increase) decrease in short-term 
           investments                             (74,223)        7,561
     Expenditures for property and equipment        (1,588)       (1,749)
                                                 _________     _________ 
     Net cash provided (used) by investing 
           activities                              (75,811)        5,812
                                                 _________     _________ 
Cash flows from financing activities:     
     Net proceeds from issuance of common stock     81,266           245
     Principal payments under equipment leases        (304)         (460)
     Increase (decrease) in long-term debt, net       (353)          (68)
                                                 _________     _________ 
     Net cash provided (used) by financing
           activities                               80,609          (283)
                                                 _________     _________ 
Net increase (decrease) in cash and cash
   equivalents                                      10,189         4,951

Cash and cash equivalents at beginning of period     4,358         2,104
                                                 _________     _________ 
Cash and cash equivalents at end of period       $  14,547     $   7,055
                                                 =========     ========= 
Reconciliation of net loss to net cash 
   provided(used) by operating activities:
     Net loss                                    $ (17,661)    $  (7,285)
     Depreciation and amortization                   1,740         1,858
     Net (increase) decrease in accounts 
       receivable and other current assets          (1,377)          (53)
     Net increase (decrease) in accounts 
          payable, accrued liabilities, 
          deferred revenue and accrued rent         22,689         4,902
                                                 _________     _________ 
     Net cash provided (used) by operating 
          activities                             $   5,391      $   (578)
                                                 =========     ========= 

                See accompanying notes to financial statements.


                         AGOURON PHARMACEUTICALS, INC.
                         NOTES TO FINANCIAL STATEMENTS
                                  (Unaudited)

1.     Nature of Operations

Agouron Pharmaceuticals, Inc. is involved in the research and development of 
novel synthetic drugs for the treatment of cancer, viral diseases and immuno-
inflammatory disease.  The Company intends to commercialize any successfully 
developed products through its own direct sales and marketing activities in 
certain markets or, when appropriate, through manufacturing and marketing 
relationships with other pharmaceutical companies.
  
2.     Financial Statements and Estimates

The balance sheet as of March 31, 1996 and the statements of operations and 
cash flows for the three-month and nine-month periods ended March 31, 1996 
and 1995 have been prepared by the Company and have not been audited.  Such 
financials, in the opinion of management, include all adjustments (consisting 
only of normal, recurring accruals) necessary to present fairly the financial 
position, results of operations and cash flows for all periods presented.  
These financial statements should be read in conjunction with the financial 
statements and notes thereto included in the Company's June 30, 1995 Annual 
Report on Form 10-K.  Interim operating results are not necessarily 
indicative of operating results for the full year.

The preparation of financial statements in conformity with generally accepted 
accounting principles requires management to make estimates and assumptions 
that affect the reported amounts of assets, liabilities, revenues and 
expenses and related disclosures as of the date of the financial statements.  
Actual results could differ from such estimates.

At March 31, 1996, it has been assumed that the existing collaborations with 
Japan Tobacco Inc. ("JT") will continue in accordance with their agreement 
terms.  As such, approximately $24,216,000 of cash received from JT has been 
classified as deferred contract revenue and is being recognized as revenue on 
a prospective basis as collaborative program expenses are incurred.  Should 
any of the underlying collaborations be terminated in advance of their 
contract terms, any deferred contract revenues related to such collaborations 
would immediately be recognized as revenue by the Company.

3.     Short-term Investments

Included in short-term investments at March 31, 1996 and June 30, 1995 is 
$1,544,000 and $172,000 of accrued interest receivable.  Included in short-
term investments at March 31, 1996 is $400,000 which has been pledged as 
collateral for certain long-term debt obligations.  At March 31, 1996, the 
Company's short-term investments are generally available for sale, are 
carried at amortized cost which approximates market, consist principally of 
United States government securities (70%) and corporate obligations (14%), 
and have average maturities of less than one year.






4.     Statement of Cash Flows

Non-cash financing activities were comprised of capital lease obligations of 
$457,000 and $17,000, respectively, in the nine-month periods ended March 31, 
1996 and 1995.

5.     Certain Concentrations

A significant portion of the Company's research and development expenditures 
are related to programs funded in whole or in part by JT.  The termination of 
such collaborative research and development programs could result in the 
absence of any prospective funding for such programs and the need to evaluate 
the level of future program spending, if any. 
Item 2.     Management's Discussion and Analysis of Financial Condition
            and Results of Operations

When used in this discussion, the words "believes", "anticipated" and similar 
expressions are intended to identify forward-looking statements.  Such 
statements are subject to certain risks and uncertainties which could cause 
actual results to differ materially from those projected.  See "Important 
Factors Regarding Forward-Looking Statements" attached as Exhibit 99 to the 
Company's quarterly report on Form 10-Q for the period ended December 31, 
1995 and incorporated herein by reference.  Readers are cautioned not to 
place undue reliance on these forward-looking statements which speak only as 
of the date hereof.  The Company undertakes no obligation to publicly release 
the result of any revisions to these forward-looking statements which may be 
made to reflect events or circumstances after the date hereof or to reflect 
the occurrence of unanticipated events.

Financial Condition

The Company relies principally on equity financings and corporate 
collaborations to fund its operations and capital expenditures.  At March 31, 
1996, due principally to the receipt of a $24,000,000 milestone payment from 
Japan Tobacco, Inc. ("JT") in August 1995, and the net proceeds of 
approximately $78,589,000 from a public offering of common stock in September 
1995, the Company had cash, cash equivalents and short-term investments of 
approximately $104,656,000.  Management believes that its present capital 
resources, plus the funding from certain existing collaborative 
relationships, will be sufficient to meet its working capital needs at least 
through 1996.  The Company will require additional long-term financing to 
meet the operating needs of 1997 and beyond.  The Company will consider 
various financing vehicles to meet such needs including collaborative 
arrangements and public offerings or private placements of Company common or 
preferred stock.  If such vehicles are not available, the Company may be 
required to delay or eliminate expenditures for certain of its products or to 
license third parties to commercialize products or technologies that the 
Company would otherwise seek to develop itself.

Results of Operations

The Company is engaged in the research and development of human 
pharmaceuticals utilizing protein structure-based drug design.  Such research 
and development has been funded from the Company's equity-derived working 
capital and through various collaborative arrangements.  The Company's net 
operating losses reflect primarily the result of its independent research and 

continued increasing investment in clinical development activities 
concentrated on the Company's lead compounds in cancer and AIDS.  As product 
sales may not begin prior to calendar 1997 and certain programs are expanding 
their preclinical and clinical development activities, it is anticipated that 
net operating losses will continue and possibly increase through fiscal 1997.

The increase in the net losses for the three and nine months ended March 31, 
1996 compared to the year-earlier periods is due principally to the Company's 
commitment to support expanding clinical activities and establish a 
commercial infrastructure associated with the Company's two leading product 
candidates.  These spending increases were only partially offset by increased 
revenues.

Contract revenues in the current nine-month period have increased compared to 
the year earlier period due mainly to an anti-HIV collaboration with JT 
initiated in December 1994. Interest income has increased significantly from 
the prior-year three- and nine-month periods due to a higher average 
investment portfolio balance resulting from the previously described public 
offering and milestone payment.

Research and development costs and expenses increased from the prior-year 
three- and nine-month periods due generally to increasing average research 
and development staff levels (approximately 22% and 20%, respectively) and 
staff-related expenditures, including occupancy, and significantly increased 
expenditures for human clinical trial activities associated with the 
Company's leading product development programs, THYMITAQ (TM) and VIRACEPT (TM).

The increase in general and administrative costs and expenses in the current 
three- and six-month periods is due chiefly to increasing average staff 
levels (approximately 36% and 25%, respectively) and staff related 
expenditures and certain costs associated with a growing sales and marketing 
infrastructure.

Interest expense in the current-year periods is generally decreasing as the 
level of debt and capital lease obligations declines.  These declines are 
partially or wholly offsetting the exercise costs associated with  certain 
lease buy-out options.





















PART II.     OTHER INFORMATION

Item 1.      Legal Proceedings:  The Company is involved in certain legal or 
             administrative proceedings generally incidental to its normal 
             business activities.  While the outcome of any such proceedings 
             cannot be accurately predicted, the Company does not believe the 
             ultimate resolution of any such existing matters should have a 
             material adverse effect on its financial position.

Item 2.      Changes in Securities:  None.

Item 3.      Defaults Upon Senior Securities:  None.

Item 4.      Submission of Matters to a Vote of Security Holders:  None.

Item 5.      Other Information:  None.

Item 6.      Exhibits and Reports on Form 8-K:
          

             a.     Exhibits:
               
                    10.59     First Amendment to Agreement Three effective 
                              February 29, 1996 between Japan Tobacco, Inc. 
                              and the Company.

                    10.60     Amendment effective January 1, 1996 to the 
                              Agouron Pharmaceuticals, Inc. 401(k) Plan.

                    27        Financial Data Schedule.  (Exhibit 27 is 
                              submitted as an exhibit only in the electronic 
                              format of this Quarterly Report on Form 10-Q 
                              submitted to the Securities and Exchange 
                              Commission.)

          b.     Reports on Form 8-K:  None.






















                                 SIGNATURE

     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.


                                   AGOURON PHARMACEUTICALS, INC.




Date:  April 26, 1996             /s/ Steven S. Cowell     
                                  ------------------------------------------
                                  Steven S. Cowell
                                  Vice President, Finance and Chief Financial
                                  Officer and Chief Accounting Officer