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

                                    FORM 10-Q

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

                For the quarterly period ended December 31, 1997


                         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 of principal executive offices)             (Zip Code)

                                 (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: As of December 31, 1997, the
registrant had 30,632,448 shares of Common Stock, no par value, outstanding.





                          AGOURON PHARMACEUTICALS, INC.

                                      INDEX



                                                                                    
                                                                                          Page No.

Part I.           Financial Information

Item 1.           Financial Statements

                  Consolidated Balance Sheet -                                                  3
                         December 31, 1997 and June 30, 1997

                  Consolidated Statement of Income (Loss) -                                     4
                         Three and Six Months Ended
                         December 31, 1997 and 1996

                  Consolidated Statement of Cash Flows-                                         5
                         Six Months Ended December 31, 1997 and 1996

                  Notes to Consolidated Financial Statements                                    6

Item 2.           Management's Discussion and Analysis of Financial                            10
                         Condition and Results of Operations


Part II.          Other Information

Item 1.           Legal Proceedings                                                            14

Item 2.           Changes in Securities                                                        14

Item 3.           Defaults Upon Senior Securities                                              14

Item 4.           Submission of Matters to a Vote of Security Holders                          14

Item 5.           Other Information                                                            14

Item 6.           Exhibits and Reports on Form 8-K                                             15

                  Signature                                                                    16


                                       2



PART I.           FINANCIAL INFORMATION

Item 1.           Financial Statements

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


   

                                                                      December 31,                June 30,
                                                                              1997                    1997
                                                                      ------------           -------------
ASSETS                                                                 (unaudited)
                                                                                       
Current assets:
     Cash and cash equivalents                                        $       29,533         $      52,484
     Short-term investments                                                   87,716                38,833
     Accounts receivable, net                                                 43,200                31,375
     Inventories                                                              78,919                58,800
     Current deferred tax assets                                                 407                   500
     Other current assets                                                      2,757                 2,209
                                                                      --------------         -------------

     Total current assets                                                    242,532               184,201

Property and equipment,  net of accumulated
     depreciation and amortization of $19,802 and $16,161                     28,327                22,613

Deferred tax assets                                                           56,843                56,000

Purchased intangibles                                                          3,800                 4,100
                                                                      --------------         -------------

                                                                      $      331,502         $     266,914
                                                                      ==============         =============
LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                                                 $       41,476         $      28,833
     Accrued liabilities                                                      24,262                 8,889
     Deferred revenue and advances                                            40,141                27,567
     Current deferred tax liabilities                                            806                   600
     Loan payable and current portion of long-term debt                        3,345                 2,526
                                                                      --------------         -------------

     Total current liabilities                                               110,030                68,415
                                                                      --------------         -------------

Long-term liabilities:
     Long-term debt, less current portion                                      4,818                 5,940
     Accrued rent                                                              1,158                 1,277
                                                                      --------------         -------------

     Total long-term liabilities                                               5,976                 7,217
                                                                      --------------         -------------

Stockholders' equity:
     Common stock, no par value, 75,000,000 shares authorized,
       30,632,448 and 29,429,920 shares issued and outstanding               332,795               317,133
     Accumulated deficit                                                    (117,299)             (125,851)
                                                                      --------------         -------------

     Total stockholders' equity                                              215,496               191,282
                                                                      --------------         -------------

                                                                      $      331,502         $     266,914
                                                                      ==============         =============


See accompanying notes to consolidated financial statements.

                                       3



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






                                                 Three Months Ended             Six Months Ended
                                            ---------------------------    --------------------------
                                                    December 31,                  December 31,
                                            ---------------------------    --------------------------
                                                                              
                                                1997           1996            1997           1996
                                            -----------     -----------    -----------    -----------

Revenues:
   Product sales                            $    91,800     $         0    $   171,302     $        0
   Contracts                                     12,462          15,109         22,465         32,623
   License fees and royalties                       400               0          2,752              0
                                            -----------     -----------    -----------     ----------

                                                104,662          15,109        196,519         32,623
                                            -----------     -----------    -----------     ----------

Operating expenses:
   Cost of product sales                         37,942               0         72,015              0
   Research and development                      30,322          23,302         57,254         52,936
   Selling, general and administrative           14,045           5,786         26,591          9,522
   Royalties                                     15,432               0         28,808              0
                                            -----------     -----------    -----------     ----------

                                                 97,741          29,088        184,668         62,458
                                            -----------     -----------    -----------     ----------

Operating income (loss)                           6,921         (13,979)        11,851        (29,835)
                                            -----------     -----------    -----------     ----------

Other income (expenses):
   Interest and other income                      1,488           1,745          2,769          3,524
   Interest expense                                (206)            (16)          (367)           (80)
                                            -----------     -----------    -----------     ----------

                                                  1,282           1,729          2,402          3,444
                                            -----------     -----------    -----------     ----------

Income (loss) before income taxes                 8,203         (12,250)        14,253        (26,391)

Income tax provision                              3,281             306          5,701            612
                                            -----------     -----------    -----------     ----------

Net income (loss)                           $     4,922     $   (12,556)   $     8,552     $  (27,003)
                                            ===========     ===========    ===========     ==========

Earnings (loss) per share:
      Basic                                 $       .16     $     (.46)    $       .28     $    (1.03)
                                            ===========     ==========     ===========     ==========
      Diluted                               $       .15     $     (.46)    $       .26     $    (1.03)
                                            ===========     ==========     ===========     ==========


Shares used in calculation of:
      Basic                                      30,520          27,048         30,242         26,100
      Diluted                                    33,238          27,048         33,298         26,100


See accompanying notes to consolidated financial statements.
                                       4




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




                                                                                         Six Months Ended
                                                                                  --------------------------
                                                                                           December 31,
                                                                                  --------------------------
                                                                                      1997         1996
                                                                                  -----------   ------------
                                                                                           

Cash flows from operating activities:
     Cash received from product sales, contracts, license fees
       and royalties                                                              $   197,268    $    24,735
     Cash paid to suppliers, employees and service providers                         (173,470)       (84,701)
     Interest received                                                                  2,769          3,524
     Interest paid                                                                       (367)           (80)
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                                  26,200        (56,522)
                                                                                  -----------    -----------

Cash flows from investing activities:
     Proceeds from maturities/sales of short-term investments                          56,824         51,266
     Purchases of short-term investments                                             (105,707)       (68,913)
     Purchases of property and equipment                                               (9,382)        (3,937)
                                                                                  ------------   -----------

     Net cash provided (used) by investing activities                                 (58,265)       (21,584)
                                                                                  -----------    -----------

Cash flows from financing activities:
     Net proceeds from issuance of common stock                                         9,417         78,741
     Principal payments under equipment leases                                           (327)           (76)
     Increase (decrease) in long-term debt, net                                            24           (183)
                                                                                  -----------    -----------

     Net cash provided (used) by financing activities                                   9,114         78,482
                                                                                  -----------    -----------

Net increase (decrease) in cash and cash equivalents                                  (22,951)           376

Cash and cash equivalents at beginning of period                                       52,484         16,451
                                                                                  -----------    -----------

Cash and cash equivalents at end of period                                        $    29,533    $    16,827
                                                                                  ===========    ===========

Reconciliation  of net income  (loss) to net cash  provided  (used) by operating
  activities:
     Net income (loss)                                                            $     8,552    $   (27,003)
     Depreciation and amortization                                                      3,968          1,529
     Provision for deferred income taxes                                                5,701              0
     Net (increase) decrease in accounts receivable
       and other current assets                                                       (12,373)        (2,755)
     Net (increase) decrease in inventories                                           (20,119)       (21,400)
     Net increase (decrease) in accounts payable, accrued liabilities,
       deferred revenue and advances, and other liabilities                            40,471         (6,893)
                                                                                  -----------    ------------

     Net cash provided (used) by operating activities                             $    26,200    $   (56,522)
                                                                                  ===========    ===========



See accompanying notes to consolidated financial statements.
                                       5





                          AGOURON PHARMACEUTICALS, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                               (December 31, 1997)


Note 1 - The Company and its significant accounting policies

The Company

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 HIV protease
inhibitor  which was cleared for  marketing  by the United  States Food and Drug
Administration  ("FDA") in March 1997. The Company intends to commercialize  any
subsequently developed products through its own direct sales and marketing force
in certain markets or, when  appropriate,  through  manufacturing  and marketing
relationships with other pharmaceutical companies.

Principles of consolidation

The consolidated  financial  statements  include the accounts of the Company and
its  wholly-owned  subsidiaries.   All  significant  intercompany  accounts  and
transactions have been eliminated.

Financial statements and estimates

The  consolidated  balance  sheet as of December  31, 1997 and the  consolidated
statements of income  (loss) and cash flows for the three and six-month  periods
ended  December 31, 1997 and 1996 have been prepared by the Company and have not
been audited. Such financial statements,  in the opinion of management,  include
all  adjustments  necessary  for their  fair  presentation  in  conformity  with
generally accepted accounting  principles.  These financial statements should be
read in conjunction with the financial  statements and notes thereto included in
the Company's June 30, 1997 Annual Report on Form 10-K. Certain  information and
footnote  disclosures  normally  included in  financial  statements  prepared in
accordance with generally accepted accounting  principles have been condensed or
omitted   pursuant  to  the  Securities  and  Exchange   Commission   rules  and
regulations.  Interim results are not necessarily  indicative of 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, 1997, it has been assumed that the existing  collaborations with
Japan  Tobacco Inc.  ("JT") will  continue in  accordance  with their  agreement
terms.  As such,  approximately  $34,962,000  of cash  received from JT has been
classified as deferred contract revenue.  Approximately  $28,157,000 of the cash
received from JT represents JT's advance
                                       6



of the Company's VIRACEPT development funding obligation through June 1998. Such
amounts are to be repaid by the Company out of future profits, if any, generated
by sales of VIRACEPT in the United  States.  The balance of the payments from JT
are non-refundable and are being recognized as contract revenue on a prospective
basis generally as collaborative  program  expenses are incurred.  Should any of
the underlying collaborations with JT be terminated in advance of their contract
terms, any deferred  contract revenues related to such  collaborations  would be
recognized as revenue by the Company.

In December 1997,  Agouron and Hoffmann-La  Roche Inc. and F. Hoffmann-La  Roche
Ltd  ("Roche")  agreed  to  end  their  anti-cancer   research  and  development
collaboration  which began in June 1996.  Agouron  has  regained  all  marketing
rights  to  its   anti-cancer   drugs   previously   within  the  scope  of  the
collaboration.  Included in deferred  contract  revenue at December  31, 1997 is
approximately $4,322,000 of cash received from Roche which will be recognized as
contract revenue by the end of fiscal 1998 on a pro-rata basis.

Inventories

The inventories consist of the following components:



                                                               December 31,          June 30,
                                                                       1997              1997
                                                              -------------    --------------
                                                                          
    

         Raw materials and work in process                    $      71,720     $      57,883
         Finished goods                                               7,199               917
                                                              -------------     -------------

                                                              $      78,919     $      58,800
                                                              =============     =============


Product sales

In March  1997,  the  Company  received  clearance  from the FDA to  market  its
anti-HIV drug, VIRACEPT.  The Company has the exclusive right to market VIRACEPT
in North  America.  Accordingly,  the  Company  ships  VIRACEPT  to  wholesalers
throughout the United States, and recognizes sales revenue upon shipment.  Sales
are reported net of discounts, rebates, chargebacks and product returns.

Also  included  in  product  sales for the three and  six-month  periods  ending
December 31, 1997 are approximately $7,292,000 and $11,420,000 of sales (at cost
plus contractually determined mark-ups) to Roche of clinical and commercial drug
supplies to be used by Roche in its licensed territory.

License fees and royalties

License fees are  recognized  as revenue  when earned as generally  evidenced by
certain factors including:  receipt of such fees, the  non-refundable  nature of
such fees, and the  satisfaction of any performance  obligations.  In July 1997,
the Company and JT granted Roche certain exclusive rights to VIRACEPT in several
Asian  countries.  For such  rights,  the Company has  received a license fee of
$2,000,000 and will, upon approval in one of the Asian  territories,  receive an
additional license fee of $1,000,000 and subsequent royalties.
                                       7




For the three and six-month  periods  ending  December 31, 1997, the Company has
accrued  and/or  received  royalties  of  approximately  $400,000  and  $752,000
resulting  from  Roche's  estimated  and actual net sales of VIRACEPT in certain
countries within their licensed territory.

Income tax provision

The Company  records a provision for current and deferred income taxes using the
liability method.

Earnings (loss) per share

In February 1997, the Financial  Accounting  Standards Board issued Statement of
Financial  Accounting  Standards No. 128 "Earnings Per Share" ("FAS 128"), which
establishes  new  standards  for  computing  earnings per share and which became
effective for financial  statements  for periods ending after December 15, 1997,
including  interim periods.  Under the new requirements,  historically  reported
"primary" and "fully diluted" earnings per share have been replaced with "basic"
and "diluted" earnings per share.

Basic  earnings  (loss) per share is based upon the weighted  average  number of
common shares outstanding during a period.  Diluted earnings (loss) per share is
based upon the weighted average number of common shares outstanding and dilutive
common stock equivalents  during a period.  Common stock equivalents are options
under the  Company's  stock  option plans which are included in the earnings per
share  computation under the treasury stock method and common shares expected to
be issued under the Company's employee stock purchase plan.

Common stock equivalents of approximately 2,718,000 and 3,056,000 shares for the
three and  six-month  periods  ended  December  31, 1997 were used to  calculate
diluted earnings per share.  For the three and six-month  periods ended December
31, 1996,  common stock  equivalents  of  approximately  2,735,000 and 2,358,000
shares were not used to calculate  diluted  earnings (loss) per share because of
their  anti-dilutive  effect.  There are no reconciling items in calculating the
numerator for basic and diluted earnings (loss) per share for any of the periods
presented.

Certain concentrations

A portion of the Company's research and development  expenditures are related to
programs  funded in whole or in part by corporate  partners.  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.
                                       8




Note 2 - Commitments

During the first quarter of fiscal 1998, the Company secured a commitment from a
commercial  bank  for a  $20,000,000  revolving  line of  credit  to be used for
general corporate purposes.  As of December 31, 1997, borrowings under this line
of credit were approximately $2,600,000.


Note 3 - Stockholders' equity

In August 1997,  outstanding shares of common stock were split two-for-one.  All
prior period share and per share amounts have been restated to reflect the stock
split.
                                       9





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

When used in this discussion,  the words  "believes,"  "anticipates" 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, 1997 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.

Overview

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  principally  funded from the Company's
equity-derived  working capital,  various  collaborative  arrangements and, most
recently, from the gross margin contribution of its first product,  VIRACEPT(R).
The  net  income  reported  in  the  current  three  and  six-month  periods  is
principally due to the  commercialization  of VIRACEPT while the Company's prior
net operating  losses reflect  primarily the result of its independent  research
and  substantial  investment  in the  clinical  and  commercial  development  of
VIRACEPT and certain anti-cancer compounds.

In March 1997, the Company received  approval from the FDA to market VIRACEPT in
the United States. For the current three and six-month periods,  due principally
to the increasing product contribution from VIRACEPT sales, the Company realized
net income of $4,922,000 and $8,552,000.

Results of Operations

Product sales

Product  sales for the current three and  six-month  periods were  approximately
$91,800,000  and  $171,302,000.  The Company  anticipates  continuing  growth in
VIRACEPT  sales during fiscal 1998 and that VIRACEPT  sales in the United States
will approximate $350,000,000 to $360,000,000 for the fiscal year.
                                       10




Contract revenues

Collaborative research and development agreements with Japan Tobacco Inc. ("JT")
and Hoffmann-La Roche Inc. and F. Hoffmann-La  Roche Ltd (collectively  "Roche")
accounted for substantially all of the Company's contract revenues for the three
and six-month  periods ended December 31, 1997 and 1996. Total contract revenues
for the three and  six-month  periods  decreased  approximately  18% and 31% due
principally  to  decreased  VIRACEPT  program  spending  by  Agouron,  which was
partially  funded by JT, and increased  spending by JT and Roche on the VIRACEPT
and  AG3340  development  programs,  which  was  partially  funded  by  Agouron.
Additionally,  the  amortization  to  revenue  over a 24  month  period  of JT's
$24,000,000 milestone payment,  which was received in August 1995, was completed
in June 1997.

In December 1997, the Company agreed to end its collaboration  with Roche in the
field of cancer. As a result of the termination agreement,  Agouron has regained
all marketing rights to its anti-cancer drugs previously within the scope of the
Roche collaboration.  The Company does not foresee any significant impact on its
financial  results for the current  fiscal year due to  termination of the Roche
collaboration  since  a  substantial  portion  of the  anticipated  fiscal  1998
anti-cancer  research and development costs of such collaboration will have been
offset by contract  funding  received from Roche.  The Company  anticipates that
contract revenues for fiscal 1998 will approximate $42,000,000.

License fees and royalties

In July 1997,  the  Company  received  a  $2,000,000  license  fee from Roche as
partial  consideration  for the grant of  VIRACEPT  marketing  rights in certain
Asian territories.

Royalty revenues of approximately  $400,000 and $752,000 have been recognized in
the current  three and  six-month  periods based on Roche's sales of VIRACEPT in
certain  countries in their licensed  territory.  The Company  anticipates  that
license fees and royalties  for fiscal 1998 will  approximate  $18,000,000,  due
primarily to the expected approval of VIRACEPT in Europe.

Cost of product sales

The  aggregate  cost of  product  sales as a  percentage  of  product  sales was
approximately 41% and 42% for the three and six-month periods ended December 31,
1997.  Gross margins on United States  commercial sales were  approximately  63%
during the current  quarter and 62% for the six months ended  December 31, 1997.
The Company  anticipates  that gross margins on United States  commercial  sales
will approximate 64% for fiscal 1998.

Research and development

Research  and  development  spending  increased  from the prior year periods due
generally to costs associated with principally  increasing  average staff levels
and staff related spending, the
                                       11



acquisition  of Alanex during the fourth  quarter of fiscal 1997, and increasing
expenses  associated  with the clinical  development of certain of the Company's
anti-cancer compounds.

In  December  1997,  the  Company   discontinued   further  development  of  its
anti-cancer drug AG337 (THYMITAQ(TM),  nolatrexed  dihydrochloride) on the basis
of its interim  analysis of results from phase II/III  trials of the drug and in
order to concentrate available resources on the development of two earlier-stage
anti-cancer agents that the Company believes have greater commercial  potential.
The Company  believes that the termination of the THYMITAQ  development  program
will not have a significant impact on current year operating results.

Selling, general and administrative

Selling,  general and administrative costs have increased substantially from the
prior year periods due principally to increasing staff levels (notably the sales
force and other marketing  personnel) and staff-related  expenditures in support
of ongoing  VIRACEPT sales and marketing  activities  subsequent to its approval
and commercial launch in March 1997. The Company anticipates that total selling,
general and  administrative  expenses will exceed $58,000,000 in fiscal 1998 due
to the full-year  effect of fiscal 1997 staff  additions,  additional  occupancy
costs,  increasing  sales and marketing  activities  and the support of VIRACEPT
Phase IV marketing studies.

Royalties

The  Company's  obligation  to share  VIRACEPT  profits  with JT is reflected in
royalty  expense  for the current  three and  six-month  periods and  represents
approximately 18% of United States product sales. It is anticipated that royalty
expense for the third and fourth  quarters of fiscal 1998 will range from 18% to
21% of United States product sales.

Other income (expense)

Interest  income has decreased in the current year periods due  principally to a
lower  average  investment  portfolio  balance.  The  prior  year's  first  half
portfolio  balance was  favorably  impacted by the July 1996 public  offering of
$77,000,000 and receipt of $15,000,000 in license fees from Roche in June 1996.

Income tax provision

The income tax  provision  in the  current  quarter has been  computed  using an
effective,  combined  federal and state rate of 40%. The cash obligation of such
provision  has been offset by the  utilization  of  deductions  generated by the
exercise  of stock  options  and/or the  utilization  of deferred  tax  benefits
(comprised mostly of net operating loss carryforwards and research tax credits).
The   Company's   accumulated   net  deferred  tax  assets  have   increased  to
approximately  $56,400,000 at December 31, 1997 due to the  realization of stock
option  exercise  deductions.  As  required  by  generally  accepted  accounting
principles, the benefit of stock option exercise deductions has been recorded to
stockholders' equity.
                                       12





Liquidity and Capital Resources

The  Company  has  relied   principally  on  equity   financings  and  corporate
collaborations to fund its operations and capital  expenditures.  In March 1997,
the  Company  received  clearance  from the FDA to  market  its  anti-HIV  drug,
VIRACEPT.  Commercial  sales of VIRACEPT for the quarters  ending June 30, 1997,
September  30,  1997  and  December  31,  1997  resulted  in  gross  margins  of
approximately $24,992,000,  $45,429,000 and $53,858,000. The Company anticipates
that net sales of VIRACEPT  will  increase  from  quarter to quarter  through at
least fiscal 1998 and provide an increasingly  significant  contribution  toward
funding the Company's operations.

At December  31,  1997,  the Company  had net working  capital of  approximately
$132,502,000,  an  increase  of  $16,716,000  over  June  30,  1997  levels  due
principally to the Company's  pre-tax  profit of  $14,253,000  and $9,417,000 in
proceeds  from  employees'  exercise  of  stock  options,  partially  offset  by
$9,382,000 in purchases of property and equipment.  Individual  working  capital
components  significantly  impacted by the commercialization of VIRACEPT include
trade accounts receivable (an increase of $15,546,000), inventories (an increase
of  $20,119,000),  accounts  payable (an  increase of  $12,643,000)  and accrued
liabilities (an increase of  $15,373,000,  due to accrued  royalties  payable to
JT).  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 December 31, 1997, the Company had cash, cash equivalents and
short-term investments of approximately $117,249,000.  The Company believes that
its current capital resources,  anticipated VIRACEPT product sales contribution,
existing   contractual   commitments  and  established   credit  facilities  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 operating
needs beyond 1998 if its  commercial  activities  do not  generate  significant,
positive  operating  results on a consistent and timely basis or if the scope of
its  research,   development,   manufacturing   or   commercial   operations  is
substantially increased. 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  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.
                                       13




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:

                  The  Company  held  its  Annual  Meeting  of  Shareholders  on
                  November 6, 1997.  At the meeting,  the  shareholders  elected
                  nine  directors  to serve  until the next  annual  meeting and
                  ratified the selection of Price  Waterhouse LLP as independent
                  accountant  of the Company for the fiscal year ending June 30,
                  1998.

                  Of the  30,312,168  shares  of  Common  Stock  of the  Company
                  outstanding  as of the  September 23, 1997 record date for the
                  Annual Meeting (the "Outstanding Shares"), the number of votes
                  cast for and the  number of votes  withheld  or voted  against
                  each nominee for director were as follows:



                                                                                     Votes
                                                               Votes               Against or
                                                                For                 Withheld
                                                            -----------            ----------
                                                                                    
 
                  John N. Abelson                            26,664,607                27,636
                  Patricia M. Cloherty                       26,662,647                29,596
                  A. E. Cohen                                26,662,939                29,304
                  Gary E. Friedman                           26,665,589                26,654
                  Michael E. Herman                          26,658,089                34,154
                  Irving S. Johnson                          26,660,580                31,663
                  Peter Johnson                              26,664,107                28,136
                  Antonie T. Knoppers                        26,658,670                33,573
                  Melvin I. Simon                            26,666,439                25,804



                  Of the  Outstanding  Shares,  26,618,768  were  voted  for the
                  ratification  of the  selection  of  Price  Waterhouse  LLP as
                  independent accountants, 32,176 were voted against or withheld
                  and 41,299 abstained.

Item 5.           Other Information:  None
                                       14




Item 6.                    Exhibits and Reports on Form 8-K:
                  a.   Exhibits:
                       10.41      Amendment to the  Agouron-Roche  Collaboration
                                  between   F.   Hoffmann-La   Roche   Ltd   and
                                  Hoffmann-La  Roche Inc. and the Company  dated
                                  December 1, 1997.  (Confidential treatment has
                                  been  requested for portions of this agreement
                                  pursuant to an  application  dated January 14,
                                  1998, 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).

                   b.  Reports on Form 8-K:  None.
                                       15





                                    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 14, 1998                      /s/ Steven S. Cowell
                                             ----------------------
                                             Steven S. Cowell
                                             Corporate Vice President, Finance
                                             Chief Financial Officer
                                             Chief Accounting Officer

                                       16