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 December 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 
13,563,000 shares of the Company's Common Stock, no par value, were 
outstanding as of January 8, 1997. 



                        AGOURON PHARMACEUTICALS, INC.

                                    INDEX

                                                                   Page No.
                                                                   --------

Part I.     Financial Information

Item 1.          Financial Statements

                 Balance Sheet -                                      3
                      December 31, 1996 and June 30, 1996

                 Statement of Operations - Three and Six              4
                      Months Ended December 31, 1996 and 1995

                 Statement of Cash Flows-                             5
                      Six Months Ended December 31, 1996 and 1995

                 Notes to Financial Statements                        6

Item 2.     Management's Discussion and Analysis of Financial         8
                 Condition and Results of Operations


Part II.    Other Information

Item 1.     Legal Proceedings                                        10

Item 2.     Changes in Securities                                    10

Item 3.     Defaults Upon Senior Securities                          10

Item 4.     Submission of Matters to a Vote of Security Holders      11

Item 5.     Other Information                                        11

Item 6.     Exhibits and Reports on Form 8-K                         11

            Signature                                                13

                                    2


PART I.  FINANCIAL INFORMATION

Item 1.  Financial Statements

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

                                                 December 31,     June 30,
                                                         1996         1996
                                                 ------------  -----------
                                                   (unaudited)
ASSETS

Current assets:
    Cash and cash equivalents                   $    16,827    $    16,451
     Short-term investments                          92,071         74,424
     Accounts receivable                              6,151          2,966
     Inventory                                       21,400              0
     Other current assets                             1,370          1,800
                                               ------------    -----------

     Total current assets                           137,819         95,641

Property and equipment, net of
     accumulated depreciation and
     amortization of $15,241 and $13,710              9,405          6,936
                                                -----------     ----------

                                                $   147,224    $   102,577
                                                ===========    ===========

LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                           $     3,895   $      6,659
     Accrued liabilities                              4,951          4,327
     Deferred revenue                                 9,085         13,788
     Current portion of long-term debt                  348            486
                                                ------------   -----------

     Total current liabilities                       18,279         25,260
                                                ------------   -----------

Long-term liabilities:
     Long-term debt, less current portion               441            501
     Accrued rent                                     1,183          1,233
                                                -----------    -----------

     Total long-term liabilities                      1,624         1,734
                                                ------------   -----------

Stockholders' equity:
     Common stock, no par value, 75,000,000 shares
     authorized, 13,558,840 and 10,731,687 shares
     issued and outstanding                         237,369        158,628
     Accumulated deficit                           (110,048)       (83,045)
                                                -----------    -----------

     Total stockholders' equity                     127,321         75,583
                                                -----------    -----------

                                                 $   147,224   $   102,577
                                                 ===========   ===========


               See accompanying notes to financial statements.

                                    3


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



                                    Three Months Ended    Six Months Ended
                                    ------------------    ----------------
                                          December 31,        December 31,
                                    ------------------    ----------------

                                      1996     1995        1996      1995  
                                    --------  -------   --------  --------

Revenues:
     Contracts and licenses         $ 15,109  $ 9,592   $ 32,623  $ 20,555
                                    --------  -------   --------  --------
Operating expenses:
     Research and development         23,302   14,188     52,936    26,716
     Selling, general and
       administrative                  5,786      977      9,522     2,083
                                    --------  -------   --------  --------


                                      29,088   15,165     62,458    28,799
                                    --------  -------   --------  --------


Operating loss                       (13,979)  (5,573)   (29,835)   (8,244)
                                    --------  -------   --------  --------


Other income and expenses:
     Interest, net                     1,729    1,556      3,444     1,847
     Taxes                              (306)    (115)      (612)     (258)
                                    --------  -------   --------  --------


                                       1,423    1,441      2,832     1,589
                                    --------  -------   --------  --------


Net loss                            $(12,556) $(4,132)  $(27,003)  $(6,655)
                                    ========  =======   ========  ========


Net loss per common share           $  (0.93) $ (0.40)  $  (2.07)  $ (0.73)
                                    ========  =======   ========  ========


Shares used in computing net 
    loss per common share             13,524   10,432     13,050     9,076
                                    ========  =======   ========  ========










                See accompanying notes to financial statements.

                                    4


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


                                                      Six Months Ended     
                                             ------------------------------
                                                          December 31,     
                                             ------------------------------
                                                   1996              1995  
                                             ------------     -------------

Cash flows from operating activities:
     Cash received from contracts
        and licenses                         $     24,735     $     31,990
     Cash paid to suppliers, employees
        and service providers                     (84,701)         (24,039)
     Interest received                              3,524            1,994
     Interest paid                                    (80)            (147)
                                             ------------     ------------

     Net cash provided (used) by 
       operating activities                       (56,522)           9,798
                                             ------------     ------------

Cash flows from investing activities:
     Net (increase) decrease 
       in short-term investments                  (17,647)         (82,248)
     Expenditures for property and equipment       (3,937)            (905)
                                             ------------     ------------

     Net cash provided (used) by 
       investing activities                       (21,584)         (83,153)
                                             ------------     ------------

Cash flows from financing activities:     
     Net proceeds from issuance of common stock    78,741           80,105
     Principal payments under equipment leases        (76)            (218)
     Increase (decrease) in long-term debt, net      (183)            (261)
                                             ------------     ------------

     Net cash provided (used) by 
       financing activities                        78,482           79,626
                                             ------------     ------------


Net increase (decrease) in cash and
  cash equivalents                                    376            6,271

Cash and cash equivalents at
  beginning of period                              16,451            4,358
                                             ------------     ------------

Cash and cash equivalents at end of period   $     16,827     $     10,629
                                             ============     ============

Reconciliation of net loss to net cash 
  provided (used) by operating activities:
     Net loss                               $     (27,003)    $     (6,655)
     Depreciation and amortization                  1,529            1,102
     Net (increase) decrease in
       accounts receivable                         (3,185)             130
     Net (increase) decrease in inventory         (21,400)               0
     Net (increase) decrease in other 
       current assets                                 430              (48)
     Net increase (decrease) in accounts
       payable, accrued liabilities, 
       and accrued rent                            (2,190)           3,964
     Net increase (decrease) in
     deferred revenue                              (4,703)          11,305
                                             ------------     ------------

     Net cash provided (used) 
       by operating activities              $     (56,522)     $     9,798
                                             ============     ============

                  See accompanying notes to financial statements.



                                    5



                        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, AIDS and other 
serious diseases.  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 December 31, 1996 and the statements of operations 
and cash flows for the three-month and six-month periods ended December 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, 1996 Annual Report on Form 10-K.  Certain June 30, 1996 
and December 31, 1995 amounts have been reclassified to conform with the 
current year presentation.  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 December 31, 1996, it has been assumed that the existing collaborations 
with Japan Tobacco Inc. ("JT") and Hoffmann-La Roche Inc. and F. Hoffmann-
La Roche Ltd ("Roche") will continue in accordance with their agreement 
terms.  As such, approximately $9,034,000 of cash received from JT and 
Roche has been classified as deferred contract revenue, is non-refundable 
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.

In December 1996, the Company filed a New Drug Application ("NDA") with the 
United States Food and Drug Administration ("FDA") for its anti-HIV drug, 
VIRACEPT(R) (nelfinavir mesylate).  In anticipation of the approval of such 
NDA by the FDA, the Company is manufacturing commercial quantities of 
VIRACEPT and has capitalized approximately $21,400,000 of work-in-process 
inventory at December 31, 1996.  If the FDA does not approve the NDA or it 
becomes likely that the FDA will not approve the NDA, any capitalized 
VIRACEPT inventory will be expensed.

                                    6



3.     Short-term investments

Included in short-term investments at December 31, 1996 and June 30, 1996 
is $1,360,000 and $1,156,000 of accrued interest receivable.  Included in 
short-term investments at December 31, 1996 is $3,400,000 which has been 
pledged as collateral for certain commercial letters of credit or long-term 
debt obligations.  At December 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 (64%) and corporate obligations (29%), and have average 
maturities of less than one year.

Inventory

Inventory is stated at the lower of cost or market and, at December 31, 
1996, consists of work-in-process at contract manufacturers.

5.     Statement of cash flows

Non-cash financing activities were comprised of capital lease obligations 
of $61,000 and $457,000 in the six-month periods ended December 31, 1996 
and 1995.

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 and 
Roche.  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.

7.     Subsequent event

On January 17, 1997, pursuant to a binding letter of intent, the Company 
and JT granted F. Hoffmann-La Roche Ltd ("Roche") exclusive marketing 
rights for VIRACEPT in Europe and other countries outside North America, 
Japan and Asia.  For the marketing rights, Roche has paid to Agouron and JT 
an initial license fee of $18,000,000 and will pay an additional 
$22,000,000 when VIRACEPT is first approved in Europe.  Roche will also pay 
royalties based on Roche's sales of VIRACEPT or, under certain conditions, 
on combined sales of VIRACEPT and INVIRASE, Roche's HIV protease inhibitor. 
On January 24, 1997, the Company received its share of the initial license 
fee, $9,000,000.

                                    7


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 Annual Report on Form 10-K for the year ended 
June 30, 1996 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 
December 31, 1996, the Company had increased its net working capital 
position by $49,159,000 over June 30, 1996 levels to $119,540,000.  The 
increase is due principally to the net proceeds of approximately 
$77,347,000 from a public offering of common stock in July 1996, which 
contributed, in part, to an $18,023,000 increase in cash, cash equivalents 
and marketable securities, the purchase of $21,400,000 of inventory and 
satisfying the cash requirements associated with the Company's year-to-date 
net loss of $27,003,000.  At December 31, 1996, the Company had cash, cash 
equivalents and short-term investments of approximately $108,898,000.  The 
Company believes that its current capital resources and existing 
contractual commitments are sufficient to maintain its current and planned 
operations through fiscal 1998.  This belief is based on current research 
and clinical development plans, anticipated working capital requirements 
associated with the planned commercial launch of VIRACEPT during fiscal 
1997, anticipated VIRACEPT product contribution subsequent to its 
commercial launch, the current regulatory environment, historical industry 
experience in the development of therapeutic drugs and general economic 
conditions.  The Company believes that additional financing may be required 
to meet the planned operating needs of fiscal 1999 if significant positive 
cash flows are not generated from commercial activities.  Such needs would 
include the expenditure of substantial funds to continue research and 
development activities, conduct existing and planned preclinical studies 
and tests, conduct human clinical trials and to support a growing 
commercial infrastructure including certain manufacturing, sales and 
marketing capabilities.  As a result, the Company anticipates pursuing 
various financing alternatives such as collaborative arrangements and 
additional public offerings or private placements of Company securities. 
If such alternatives are not available, the Company may be required to 
delay or eliminate expenditures for certain of its potential products under 
development or to license third parties to commercialize products or 
technologies that the Company would otherwise seek to develop or 
commercialize itself. 



                                    8



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 and 
commercial development activities concentrated on the Company's lead 
compounds in cancer and AIDS.  As product sales may not begin prior to 
fiscal 1998 and certain programs are expanding their preclinical, clinical, 
and commercial development activities, it is anticipated that quarterly net 
losses will continue into fiscal 1998.

The increases in the net losses for the three and six months ended December 
31, 1996 compared to the year-earlier periods are due principally to the 
Company's ongoing commitment to support significant clinical testing and 
development activities to facilitate an approvable VIRACEPT NDA during 
fiscal 1997, and to establish a commercial infrastructure to achieve a 
timely commercial launch of VIRACEPT subsequent to the anticipated approval 
of the NDA.  These spending increases were only partially offset by 
increased revenues from the JT collaboration and new revenues from the 
Roche collaboration.

Contract revenues in the current three and six-month periods have increased 
compared to the year-earlier periods due mainly to expanding clinical trial 
activities on the anti-HIV collaboration with JT and the new (June 1996) 
development collaboration with Roche. 

Research and development expenses increased from the prior-year periods due 
generally to increasing average research and development staff levels 
(approximately 42% in the three and six month periods) and staff-related 
expenditures, including occupancy, and significantly increased expenditures 
for human clinical trial activities associated with the Company's leading 
product development program, VIRACEPT.

The increase in selling, general and administrative expenses in the current 
three and six-month periods is due chiefly to increasing average staff 
levels (approximately 207% in the three month period and 171% in the six 
month period) and staff related expenditures, certain premarketing costs 
associated with the anticipated launch of VIRACEPT during fiscal 1997 and 
other costs associated with a growing sales and marketing infrastructure.

Interest (net) has increased in the current-year periods due principally to 
a higher average investment portfolio balance resulting from the previously 
described public offering.  Taxes have increased due to certain foreign 
taxes paid in conjunction with the JT collaboration. 


                                    9



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 or results of 
operations.

Item 2.     Changes in Securities:

On November 7, 1996, the Board of Directors of the Company adopted a 
Stockholder Rights Plan.  Under the terms of the Rights Plan, stockholders 
of record as of November 21, 1996, received a dividend of one Preferred 
Stock Purchase Right for each share of Common Stock held on that date.  The 
Rights will expire 10 years after issuance, and will be exercisable only if 
a person or group becomes the beneficial owner of 15% or more of the Common 
Stock (such person or group, a "15% holder") or commences a tender or 
exchange offer which would result in the offeror beneficially owning 15% or 
more of the Common Stock.  Each Right will entitle stockholders to buy one 
one-ten thousandth of a share of Series B Participating Preferred Stock of 
the Company at an exercise price of $500.00 per share subject to certain 
antidilution adjustments.

If a person or group accumulates 15% or more of the Common Stock, each 
Right (other than Rights held by a 15% holder and certain related parties, 
which will be voided) will be adjusted so that upon exercise the holder 
will have the right to receive that number of shares of Common Stock (or in 
certain circumstances, a combination of securities and/or assets) having a 
value of twice the exercise price of the Right.  In addition, if following 
the public announcement of the existence of a 15% holder the Company is 
involved in a merger or business combination or a sale of 50% or more of 
the Company's assets or earning power, each Right (other than Rights held 
by a 15% holder and certain related parties, which will be voided) will 
represent the right to purchase, at the exercise price, common stock of the 
acquiring entity having a value of twice the exercise price at the time. 
The Board of Directors will also have the right, following the public 
announcement of the existence of a 15% holder, to cause each Right (other 
than rights held by the 15% holder) to be exchanged for one share of Common 
Stock.

The Board of Directors is entitled to redeem the Rights at $0.001 per Right 
at any time prior to the public announcement of the existence of a 15% 
holder.

Item 3.     Defaults Upon Senior Securities:  None.

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

The Company held its Annual Meeting of Shareholders on November 7, 
1996 and proxies for such meeting were solicited pursuant to Regulation 
14A.  There was no solicitation in opposition to management's nominees for 
directors as listed in the proxy statement and all such nominees were 
elected.  The names of directors elected at the meeting are:  John N. 
Abelson, Patricia M. Cloherty, A. E. Cohen, Gary E. Friedman, Michael E. 
Herman, Irving S. Johnson, Peter Johnson, Antonie T. Knoppers and Melvin I. 
Simon.  Each director received at least 12,132,574 votes in favor of their 
election.

     In addition, the shareholders voted on and approved two other 
proposals as listed in the proxy statement and summarized below.

1.     The shareholders approved the Company's 1996 Stock Option Plan.  The 
vote was 5,048,130 for, 2,780,424 against, 49,863 abstained and 4,352,669 
not voted.

2.     The shareholders ratified the selection of Price Waterhouse as 
certified public accountants.  The vote was 12,198,258 for, 14,305 against 
and 18,523 abstained.

Item 5.     Other Information:

On January 17, 1997, pursuant to a binding letter of intent, the Company 
and JT granted F. Hoffmann-La Roche Ltd ("Roche") exclusive marketing 
rights for VIRACEPT in Europe and other countries outside North America, 
Japan and Asia.  For the marketing rights, Roche has paid to Agouron and JT 
an initial license fee of $18,000,000 and will pay an additional 
$22,000,000 when VIRACEPT is first approved in Europe.  Roche will also pay 
royalties based on Roche's sales of VIRACEPT or, under certain conditions, 
on combined sales of VIRACEPT and INVIRASE, Roche's HIV protease inhibitor.  
On January 24, 1997, the Company received its share of the initial license 
fee, $9,000,000.

                                    10


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

Exhibits:

4.4**     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. 
10.63     Lease Amendment No. 3 dated October 16, 1996 between John Hancock 
Life Insurance Company and the Company
10.64     Sublease between The Scripps Research Institute and the Company dated 
November 4, 1996.
10.65     Premises Modification Agreement dated November 4, 1996 between 
The Scripps Research Institute and the Company
10.66     Lease dated October 25, 1996 between Scripps Jack, Ltd. and the 
Company
10.67     Form of 1990 Incentive Stock Option Agreement
10.68     Form of 1990 Non-Statutory Stock Option Agreement for 
Employees/Officers/Directors
10.69     Form of 1990 Non-Statutory Stock Option Agreement for Consultants
10.70*     1996 Stock Option Plan
10.71(     Form of 1996 Incentive Stock Option Agreement.
10.72(     Form of 1996 Non-Statutory Stock Option Agreement for 
Employees/Officers/Directors
10.73(     Form of 1996 Stock Option Agreement for Consultants
10.74     Letter of Intent between F. Hoffmann-La Roche Ltd of Basel, 
Switzerland, Japan Tobacco Inc., and the Company dated January 17, 1997. 
(Confidential treatment has been requested for portions of this agreement 
pursuant to an application dated January 27, 1997, as separately filed with 
the Securities and Exchange Commission)

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)

27A     Financial Data Schedule (amended) for fiscal year ended June 30, 
1996
27B     Financial Data Schedule (amended) for the quarter ended September 
30,1996

b.     Reports on Form 8-K:  

     A report on Form 8-K dated November 7, 1996 was filed on November 8, 
1996.  Such report related to the adoption by the Board of Directors of the 
Company of a stockholder rights plan contemplating the issuance of rights 
to purchase Series B Participating Preferred Stock to the Company's common 
shareholders of record as of November 21, 1996.


*     Incorporated by reference to Form S-8 dated November 26, 1996.
**    Incorporated by reference to Form 8-A/A filed December 20, 1996, 
File No. 001-12445.


                                    11



                                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:  January 28, 1997         /s/ Steven S. Cowell     
                                -------------------------------------------
                                Steven S. Cowell
                                Vice President, Finance and Chief Financial
                                Officer and Chief Accounting Officer


                                    12

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