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, 1997

                                    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 13,678,000 shares
of the Company's  Common Stock,  no par value,  were  outstanding as of April 4,
1997.





                          AGOURON PHARMACEUTICALS, INC.

                                      INDEX

                                                                        Page No.

Part I.       Financial Information

Item 1.       Financial Statements
                  Balance Sheet -                                             3
                         March 31, 1997 and June 30, 1996

                  Statement of Operations - Three and Nine                    4
                         Months Ended March 31, 1997 and 1996

                  Statement of Cash Flows-                                    5
                         Nine Months Ended March 31, 1997 and 1996

                  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                                          11

Item 2.            Changes in Securities                                     11

Item 3.            Defaults Upon Senior Securities                           11

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                                                  12






PART I.           FINANCIAL INFORMATION

Item 1.           Financial Statements

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


                                                                            March 31,              June 30,
                                                                                1997                   1996
                                                                          (unaudited)
ASSETS
                                                                                       
Current assets:
     Cash and cash equivalents                                         $       7,595         $      16,451
     Short-term investments                                                   75,332                74,424
     Accounts receivable                                                      16,481                 2,966
     Inventory                                                                42,657                     0
     Other current assets                                                      1,006                 1,800
                                                                       -------------         -------------

     Total current assets                                                    143,071                95,641

Property and equipment,  net of accumulated
     depreciation and amortization of $14,933 and $13,710                     11,905                 6,936
                                                                       -------------         -------------

                                                                       $     154,976         $     102,577
                                                                       =============         =============

LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                                                  $      14,015         $       6,659
     Accrued liabilities                                                       7,501                 4,327
     Deferred revenue                                                          7,489                13,788
     Current portion of long-term debt                                           427                   486
                                                                       -------------         -------------

     Total current liabilities                                                29,432                25,260
                                                                       -------------         -------------

Long-term liabilities:
     Long-term debt, less current portion                                        534                   501
     Accrued rent                                                              1,158                 1,233
                                                                       -------------         -------------

     Total long-term liabilities                                               1,692                 1,734
                                                                       -------------         -------------

Stockholders' equity:
     Common stock, no par value, 75,000,000 shares authorized,
       13,669,169 and 10,731,687 shares issued and outstanding               238,899               158,628
     Accumulated deficit                                                    (115,047)              (83,045)
                                                                       -------------         -------------

     Total stockholders' equity                                              123,852                75,583
                                                                       -------------         -------------

                                                                       $     154,976         $     102,577
                                                                       =============         =============


                 See accompanying notes to financial statements.





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




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

                                            1997          1996                  1997         1996
                                           -------    -----------           -----------    ---------
                                                                                               
Revenues:
   Net sales                          $    13,401    $        --           $    13,401     $       --
   Contracts                               16,212          6,910                48,835         27,465
   License fees                             9,000             --                 9,000             --
                                      -----------    -----------           -----------     ----------

                                           38,613          6,910                71,236         27,465
                                           ------    -----------           -----------     ----------

Operating expenses:
   Cost of sales                            6,023             --                 6,023             --
   Research and development                28,431         17,064                81,367         43,780
   Selling, general and administrative     10,280          1,968                19,802          4,051
                                      -----------    -----------           -----------     ----------

                                           44,734         19,032               107,192         47,831
                                           ------    -----------           -----------     ----------

Operating loss                             (6,121)       (12,122)              (35,956)       (20,366)
                                      -----------    -----------           -----------     ----------

Other income and expenses:
   Interest, net                            1,428          1,486                 4,872          3,333
   Taxes                                     (306)          (370)                 (918)          (628)
                                      -----------    -----------           -----------     ----------

                                            1,122          1,116                 3,954          2,705
                                            -----    -----------           -----------     ----------

Net loss                              $    (4,999)   $   (11,006)          $   (32,002)    $  (17,661)
                                      ===========    ===========           ===========     ==========

Net loss per common share             $    (0.37)    $     (1.04)          $     (2.42)    $    (1.84)
                                      ==========     ===========           ===========     ==========


Shares used in computing net loss
   per common share                        13,615         10,571                13,239          9,574
                                      ===========    ===========           ===========     ==========










                See accompanying notes to financial statements.




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


                                                                                         Nine Months Ended
                                                                                             March 31,
                                                                                        1997         1996
                                                                                           
Cash flows from operating activities:                                             
     Cash received from contracts and licenses                                    $    51,422    $    46,477
     Cash paid to suppliers, employees and service providers                         (137,043)       (44,419)
     Interest received                                                                  4,965          3,520
     Interest paid                                                                        (93)          (187)
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                                 (80,749)         5,391
                                                                                  -----------    -----------

Cash flows from investing activities:
     Net (increase) decrease in short-term investments                                   (908)       (74,223)
     Expenditures for property and equipment                                           (7,016)        (1,588)
                                                                                  ------------   -----------

     Net cash provided (used) by investing activities                                  (7,924)       (75,811)
                                                                                  -----------    -----------

Cash flows from financing activities:
     Net proceeds from issuance of common stock                                        80,271         81,266
     Principal payments under equipment leases                                           (179)          (304)
     Increase (decrease) in long-term debt, net                                          (275)          (353)
                                                                                  -----------    -----------

     Net cash provided (used) by financing activities                                  79,817         80,609
                                                                                  -----------    -----------


Net increase (decrease) in cash and cash equivalents                                   (8,856)        10,189

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

Cash and cash equivalents at end of period                                        $     7,595    $    14,547
                                                                                  ===========    ===========

Reconciliation of net loss to net cash provided (used) by operating activities:
     Net loss                                                                     $   (32,002)   $   (17,661)
     Depreciation and amortization                                                      2,475          1,740
     Net (increase) decrease in accounts receivable                                   (13,515)            (6)
     Net (increase) decrease in inventory                                             (42,657)             0
     Net (increase) decrease in other current assets                                      794         (1,371)
     Net increase (decrease) in accounts payable, accrued liabilities,
           and accrued rent                                                            10,455          3,671
     Net increase (decrease) in deferred revenue                                       (6,299)        19,018
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                             $   (80,749)   $     5,391
                                                                                  ===========    ===========


                See accompanying notes to financial statements.






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

1.       Nature of operations

Agouron Pharmaceuticals,  Inc. is an integrated pharmaceutical company committed
to the  discovery,  development,  manufacturing  and marketing of small molecule
drugs  engineered to inactivate  proteins which play key roles in cancer,  AIDS,
and other  serious  diseases.  The Company,  through its own sales and marketing
force, is currently marketing VIRACEPT(R)(nelfinavir  mesylate), an inhibitor of
the HIV protease,  which recently  received approval from the United States Food
and Drug  Administration  ("FDA").  The  Company  intends to  commercialize  any
subsequently  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, 1997 and the statements of operations and cash
flows for the three-month  and nine-month  periods ended March 31, 1997 and 1996
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 March 31, 1996  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 March 31, 1997,  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  $6,075,000 of cash received from JT and Roche has been classified
as deferred  contract  revenue,  is  non-refundable  and is being  recognized as
revenue  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.       Revenue recognition

In March  1997,  the  Company  received  clearance  from the FDA to  market  its
anti-HIV  drug,  VIRACEPT.  Accordingly,  in March,  the Company began  shipping
VIRACEPT to wholesalers  throughout the United  States.  The Company  recognizes
sales revenue upon shipment.

In January 1997,  the Company and JT granted Roche certain  exclusive  rights to
VIRACEPT in Europe and other  countries  outside North America,  Japan and Asia.
For such rights,  the Company has received an initial  license fee of $9,000,000
and will, upon approval of VIRACEPT in Europe, receive an additional license fee
and subsequent  royalties.  The license fees are  non-refundable and the Company
has no  significant  ongoing  obligation  with respect to such fees. The Company
recognizes such fees as revenue when earned.

4.       Short-term investments

Included  in  short-term  investments  at March  31,  1997 and June 30,  1996 is
$1,107,000 and $1,156,000 of accrued interest receivable. Included in short-term
investments at March 31, 1997 is $3,400,000 which has been pledged as collateral
for certain commercial letters of credit or long-term debt obligations. At March
31, 1997, 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 (62%) and corporate  obligations (30%), and
have average maturities of less than one year.

5.       Inventory

Inventory  is  stated at the lower of cost or  market  and,  at March 31,  1997,
consists  of   approximately   $42,213,000   of   work-in-process   at  contract
manufacturers  and $444,000 of finished  goods.  The Company had no inventory at
June 30, 1996.

6.   Statement of cash flows

Non-cash  financing  activities  were comprised of capital lease  obligations of
$428,000 and $457,000 in the nine-month periods ended March 31, 1997 and 1996.

7.       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.






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 this Form 10-Q.  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. However, on March 14, 1997, the
Company received  clearance from the FDA to market its anti-HIV drug,  VIRACEPT,
and commercial  sales of VIRACEPT for the quarter ending March 31, 1997 resulted
in a gross margin of approximately $7,378,000.  The Company anticipates that net
sales of  VIRACEPT  will  steadily  increase  through at least  fiscal  1998 and
provide an increasingly  significant  contribution  toward funding the Company's
operations.

At March  31,  1997,  the  Company  had net  working  capital  of  approximately
$113,639,000,  an  increase  of  $43,258,000  over  June  30,  1996  levels  due
principally  to the net  proceeds  of  approximately  $77,347,000  from a public
offering of common stock in July 1996, partially offset by the cash requirements
associated with the Company's  year-to-date net loss of $32,002,000.  Individual
working capital components  significantly  impacted by the  commercialization of
VIRACEPT  include  inventory  (an  increase  of  $42,657,000),   trade  accounts
receivable  (an increase of  $13,401,000)  and accounts  payable (an increase of
$7,356,000).  It is anticipated  that these working capital  components and cash
and  short-term  investments  will  continue  to be  significantly  impacted  as
VIRACEPT  sales  increase.  At March  31,  1997,  the  Company  had  cash,  cash
equivalents and short-term investments of approximately $82,927,000. The Company
believes that its current capital resources,  existing  contractual  commitments
and anticipated  VIRACEPT product sales  contribution are sufficient to maintain
its current  operations  through  fiscal  1998.  This belief is based on current
research  and  clinical   development   plans,   anticipated   working   capital
requirements  associated with the expanding  commercialization of VIRACEPT,  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 1998 and beyond if significant  positive cash
flows are not generated from commercial activities on a timely basis. Such needs
would  include the  expenditure  of  substantial  funds to  continue  and expand
research and development  activities,  conduct existing and planned  preclinical
studies and human clinical trials and to support the increasing  working capital
requirements of a growing  commercial  infrastructure  including  manufacturing,
sales and  marketing.  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  defer or  restrict  certain
commercial  activities,  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.

Results of Operations

The  Company is  committed  to the  discovery,  development,  manufacturing  and
marketing of human  pharmaceuticals  targeting  cancer,  AIDS, and other serious
diseases.  Operations to date have 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  substantial  investment in clinical and commercial  development  activities
concentrated on the Company's recently approved first product, VIRACEPT, and its
lead compounds in cancer.

As product sales have only recently commenced 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
Company  anticipates that quarterly  operating results will be profitable by the
end of fiscal 1998.

The net loss for the current  three-month  period has decreased  compared to the
year-earlier  period  due  primarily  to  the  gross  margin  contribution  from
commercial  sales of VIRACEPT,  a $9,000,000  license fee and a 135% increase in
contract  revenue  which  were  only  partially  offset  by a 103%  increase  in
operating  expenses.  The increase in the  year-to-date net loss compared to the
year-earlier  period is due  primarily to a  significantly  greater  increase in
operating  expenses  compared  to the  revenue  increases  described  above on a
quarterly basis.

Net sales and  related  cost of sales  reflect  the  initial  sales of  VIRACEPT
following its approval by the FDA in March 1997.  The Company  anticipates  that
gross margins on VIRACEPT sales will improve as sales increase.

Contract  revenues in the current three and  nine-month  periods have  increased
compared to the  year-earlier  periods due mainly to increased  program activity
and  spending  on the JT  collaborations  and the new  (June  1996)  development
collaborations with Roche.

License fees in the current three and nine-month  periods  represent the initial
license  fee  received  from  Roche in  January  1997 in  return  for  exclusive
marketing  rights to  VIRACEPT  in  Europe  and other  countries  outside  North
America, Japan and Asia.

Research and  development  expenses  increased from the  prior-year  periods due
generally  to  increasing   average   research  and  development   staff  levels
(approximately  40% in the  three  and  nine-month  periods)  and  staff-related
expenditures,  including occupancy,  and significantly increased expenditures in
support of human clinical trials and an expanded access program  associated with
VIRACEPT.

The  increase in selling,  general  and  administrative  expenses in the current
three and nine-month  periods is due chiefly to increasing  average staff levels
(approximately 275% in the three-month period and 216% in the nine-month period)
and  staff  related  expenditures,  certain  premarketing  and  advertising  and
promotion  costs  associated with the launch of VIRACEPT in March 1997 and other
costs associated with a growing sales and marketing infrastructure.

Interest (net) has increased in the current nine-month period 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.






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:  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:


    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)

    99.      Important Factors Regarding Forward-Looking Statements


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 14, 1997                              /s/ Steven S. Cowell
                                                   ----------------------
                                                  Steven S. Cowell
                                                  Vice President, Finance and 
                                                  Chief Financial Officer and 
                                                  Chief Accounting Officer