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, 1998


                         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 February 3, 1999,  the
registrant had  approximately  31,947,000  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, 1998 and June 30, 1998

                  Consolidated Statement of Income -                                            4
                         Three and Six Months Ended
                         December 31, 1998 and 1997

                  Consolidated Statement of Cash Flows-                                         5
                         Six Months Ended December 31, 1998 and 1997

                  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                          15

ITEM 5.           Other Information                                                            16

ITEM 6.           Exhibits and Reports on Form 8-K                                             16

                  Signature                                                                    17


                                       2



PART I.           FINANCIAL INFORMATION

ITEM 1.           FINANCIAL STATEMENTS

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



                                                                        December 31,               June 30,
                                                                                1998                   1998
                                                                        ------------               --------
ASSETS                                                                 (unaudited)

Current assets:
                                                                                                 
     Cash and cash equivalents                                        $       34,547         $      19,098
     Short-term investments                                                   39,187                68,025
     Accounts receivable, net                                                 68,560                51,341
     Inventories                                                             104,419               103,706
     Current deferred tax assets                                                 594                   564
     Other current assets                                                      2,552                 5,247
                                                                      --------------         -------------

     Total current assets                                                    249,859               247,981

Property and equipment,  net of accumulated
     depreciation and amortization of $30,431and $24,321                      46,557                47,212
Deferred tax assets                                                           71,680                64,644
Purchased intangibles                                                          3,200                 3,500
                                                                      --------------         -------------

                                                                      $      371,296         $     363,337
                                                                      ==============         =============
LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                                                 $       24,858         $      44,393
     Accrued liabilities                                                      43,577                35,356
     Deferred revenue and advances                                            17,017                23,563
     Current deferred tax liabilities                                          2,447                 1,139
     Loan payable and current portion of long-term debt                        7,880                15,802
                                                                      --------------         -------------

     Total current liabilities                                                95,779               120,253
                                                                      --------------         -------------

Long-term liabilities:
     Long-term debt, less current portion                                      6,375                 5,892
     Accrued rent                                                                864                 1,023
                                                                      --------------         -------------

     Total long-term liabilities                                               7,239                 6,915
                                                                      --------------         -------------

Stockholders' equity:
     Common stock, no par value, 75,000,000 shares authorized,
       31,738,847 and 31,053,380 shares issued and outstanding               366,626               348,482
     Accumulated other comprehensive income (expense)                           (161)                  384
     Accumulated deficit                                                     (98,187)             (112,697)
                                                                      --------------         -------------

     Total stockholders' equity                                              268,278               236,169
                                                                      --------------         -------------

                                                                      $      371,296         $     363,337
                                                                      ==============         =============


See accompanying notes to consolidated financial statements.

                                       3



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





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

                                                1998           1997            1998           1997   
                                            -----------     -----------    -----------    -----------

Revenues:
                                                                                      
   Product sales                            $   158,193     $    91,800    $   292,063     $  171,302
   Contracts                                      5,416          12,462         11,433         22,465
   Royalties and license fees                     7,100             400         12,150          2,752
                                            -----------     -----------    -----------     ----------

                                                170,709         104,662        315,646        196,519
                                            -----------     -----------    -----------     ----------

Operating expenses:
   Cost of product sales                         74,241          37,942        131,286         72,015
   Research and development                      39,345          30,322         76,709         57,254
   Selling, general and administrative           20,701          14,045         37,843         26,591
   Royalties                                     28,085          15,432         53,978         28,808
                                            -----------     -----------    -----------     ----------

                                                162,372          97,741        299,816        184,668
                                            -----------     -----------    -----------     ----------

Operating income                                  8,337           6,921         15,830         11,851
                                            -----------     -----------    -----------     ----------

Other income (expenses):
   Interest and other income                        851           1,488          1,887          2,769
   Interest expense                                (223)           (206)          (646)          (367)
                                            -----------     -----------    -----------     ----------

                                                    628           1,282          1,241          2,402
                                            -----------     -----------    -----------     ----------

Income before income taxes                        8,965           8,203         17,071         14,253

Income tax provision                              1,345           3,281          2,561          5,701
                                            -----------     -----------    -----------     ----------

Net income                                  $     7,620     $     4,922    $    14,510     $    8,552
                                            ===========     ===========    ===========     ==========

Earnings per share:
      Basic                                 $       .24     $      .16     $       .46     $      .28
                                            ===========     ==========     ===========     ==========
      Diluted                               $       .22     $      .15     $       .43     $      .26
                                            ===========     ==========     ===========     ==========


Shares used in calculation of:
      Basic                                      31,410          30,520         31,269         30,242
      Diluted                                    34,237          33,238         33,661         33,298

                                      
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,
                                                                                  --------------------------     
                                                                                      1998         1997 
                                                                                  ----------     -----------    
                                                                                           

Cash flows from operating activities:

     Cash received from product sales, contracts, royalties
       and license fees                                                           $   291,881    $   197,268
     Cash paid to suppliers, employees and service providers                         (302,271)      (173,520)
     Interest received                                                                  1,859          2,819
     Interest paid                                                                       (646)          (367)
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                                  (9,177)        26,200
                                                                                  -----------    -----------

Cash flows from investing activities:
     Proceeds from maturities/sales of short-term investments                          44,053         56,824
     Purchases of short-term investments                                              (15,760)      (105,707)
     Purchases of property and equipment                                               (6,053)        (9,313)
                                                                                  -----------    ------------

     Net cash provided (used) by investing activities                                  22,240        (58,196)
                                                                                  -----------    -----------

Cash flows from financing activities:
     Net proceeds from issuance of common stock                                         9,825          9,417
     Proceeds from credit line                                                         30,000         12,600
     Principal payments on credit line, long-term debt
       and capital leases                                                             (37,439)       (12,972)
                                                                                  -----------    -----------

     Net cash provided (used) by financing activities                                   2,386          9,045
                                                                                  -----------    -----------

Net increase (decrease) in cash and cash equivalents                                   15,449        (22,951)

Cash and cash equivalents at beginning of period                                       19,098         52,484
                                                                                  -----------    -----------

Cash and cash equivalents at end of period                                        $    34,547    $    29,533
                                                                                  ===========    ===========

Reconciliation   of  net  income  to  net  cash  provided  (used)  by  operating
  activities:
     Net income                                                                   $    14,510    $     8,552
     Depreciation and amortization                                                      7,008          3,968
     Provision for deferred income taxes                                                2,561          5,701
     Net (increase) decrease in accounts receivable
       and other current assets                                                       (14,524)       (12,373)
     Net (increase) decrease in inventories                                              (713)       (20,119)
     Net increase (decrease) in accounts payable, accrued liabilities,
       deferred revenue and advances, and other liabilities                           (18,019)        40,471
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                             $    (9,177)   $    26,200
                                                                                  ===========    ===========



See accompanying notes to consolidated financial statements.

                                       5



                          AGOURON PHARMACEUTICALS, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                               (December 31, 1998)


NOTE 1 - THE COMPANY AND ITS SIGNIFICANT ACCOUNTING POLICIES

THE COMPANY

Agouron  Pharmaceuticals,  Inc.  ("Agouron" or the  "Company") was organized and
incorporated in California in June 1984. Agouron is an integrated pharmaceutical
company committed to the discovery, development,  manufacturing and marketing of
innovative therapeutic products engineered to inactivate proteins which play key
roles in cancer, AIDS and other serious diseases.  The Company,  through its own
sales and marketing  organization,  is currently  marketing in the United States
its  first  drug,  VIRACEPT(R)   (nelfinavir  mesylate)  for  treatment  of  HIV
infection.  The Company is also conducting  pivotal phase II/III clinical trials
for AG3340 for treatment of lung and prostate cancer.  In addition,  Agouron has
initiated a phase II/III  pivotal  clinical  trial of  REMUNE(TM)  (AG1661),  an
immune-based  therapeutic  agent for  treatment of HIV  infection and AIDS being
co-developed by Agouron and The Immune Response  Corporation  ("IRC").  Further,
the Company has a number of programs in progress for discovery or development of
other new  drugs in the  fields  of  cancer,  viral  disease  and other  serious
diseases.  The  Company  is also  using  the  proprietary  core  drug  discovery
technology of Alanex Corporation  ("Alanex"),  a wholly-owned  subsidiary of the
Company,  to  accelerate  the steps  necessary to discover  small-molecule  drug
candidates,  from the initial  identification of compounds that exhibit activity
against  selected  biological  targets to the  progression of these compounds to
drug candidates for human clinical trials.

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, 1998 and the  consolidated
statements  of income and cash flows for the three and  six-month  periods ended
December  31, 1998 and 1997 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, 1998 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.

                                       6




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.

INVENTORIES

The inventories consist of the following components:



                                                               December 31,          June 30,
                                                                       1998              1998
                                                              -------------     -------------                       

                                                                                    
         Raw materials and work in process                    $      99,100     $      95,517
         Finished goods                                               5,319             8,189
                                                              -------------     -------------

                                                              $     104,419     $     103,706
                                                              =============     =============


PRODUCT SALES

The Company has the exclusive  right to market its anti-HIV drug VIRACEPT in the
United States and Canada. Accordingly, the Company ships VIRACEPT to wholesalers
throughout  the United States and certain  provinces of Canada,  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  ended
December 31, 1998 are  approximately  $45,593,000  and  $72,276,000 of sales (at
cost  plus  contractually  determined  mark-ups)  to F.  Hoffmann-La  Roche  Ltd
("Roche") of clinical and  commercial  drug  supplies to be used by Roche in its
licensed territory. For the three and six-month periods ended December 31, 1997,
sales to Roche  were  approximately  $7,292,000  and  $11,420,000.  The  Company
receives a royalty on Roche's subsequent commercial sales of such drug supplies.

ROYALTIES AND LICENSE FEES

Royalty  revenues are recognized based on estimated and actual sales of licensed
products in licensed territories.

For the three and  six-month  periods ended  December 31, 1998,  the Company has
accrued and/or received  royalties of  approximately  $6,800,000 and $11,725,000
resulting  from  estimated  and actual net sales of VIRACEPT by Roche within its
licensed territory. For the three and six-month periods ended December 31, 1997,
Roche royalties were approximately $400,000 and $752,000.

License fees are  recognized  as revenue  when earned as generally  evidenced by
certain factors including: receipt of such fees, satisfaction of any performance
obligations  and the  non-refundable  nature of such fees.  In August 1998,  the
Company and JT granted Roche certain exclusive rights to VIRACEPT in Mexico. For
such  rights,  the Company  realized  as revenue a license fee of $125,000  from
Roche. In December 1998, the Company granted to Zarix
                                       7



Limited, a biopharmaceutical  development  company,  certain exclusive rights to
THYMITAQ,  an anti-cancer drug. For such rights, the Company realized as revenue
a license fee of $300,000.

INCOME TAX PROVISION

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

EARNINGS PER SHARE

Basic  earnings  per share is based upon the weighted  average  number of common
shares outstanding during a period. Diluted earnings 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 2,827,000 and 2,392,000 shares for the
three and  six-month  periods  ended  December  31, 1998 were used to  calculate
diluted earnings per share.  For the three and six-month  periods ended December
31, 1997,  common stock  equivalents  of  approximately  2,718,000 and 3,056,000
shares  were  used  to  calculate  diluted  earnings  per  share.  There  are no
reconciling  items in calculating  the numerator for basic and diluted  earnings
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  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.

NOTE 2 - COMPREHENSIVE INCOME

As of July 1, 1998,  the  Company  adopted  Statement  of  Financial  Accounting
Standards  No.  130  ("FAS  130"),   "Reporting   Comprehensive  Income,"  which
establishes new rules for the reporting and display of comprehensive  income and
its components.  FAS 130 requires  unrealized  gains and losses on the Company's
available-for-sale  securities to be included in other comprehensive income. The
Company presents such information in its statement of stockholders' equity on an
annual basis and in a footnote in its  quarterly  reports.  During the three and
six-month  periods  ended  December 31,  1998,  total  comprehensive  income was
$7,227,000 and $13,965,000, respectively. During the three and six-month periods
ended  December  31,  1997,  total  comprehensive   income  was  $4,922,000  and
$8,552,000.

                                       8



NOTE 3 - SUBSEQUENT EVENT

On January 26,  1999,  the  Company  announced  that it had signed a  definitive
agreement to merge with  Warner-Lambert  Company, a worldwide company devoted to
discovering,  developing,  manufacturing, and marketing quality pharmaceuticals,
consumer healthcare,  and confectionary  products.  Warner-Lambert  employs more
than 40,000 people worldwide.  The proposed merger, which is subject to approval
by Agouron's shareholders and federal regulators,  will be treated as a "pooling
of interests" for accounting purposes. If approved, each share of Agouron common
stock  will be  converted  into the right to  receive  that  number of shares of
Warner-Lambert  common stock equal to $60.00 divided by an average closing sales
price of Warner-Lambert  common stock prior to the effective date of the merger,
except that such ratio will not be less than .8108 or more than .9300.

                                       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  (including those associated with
continued  growth of VIRACEPT  sales,  the impact of  competitive  products  and
regulatory approvals) 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, 1998 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  VIRACEPT.  The net  income
reported in the three and six-month  periods ended December 31, 1998 and 1997 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,  VIRACEPT  was approved for  marketing in the United  States.  In
January 1998, March 1998 and August 1998, VIRACEPT was approved for marketing in
Europe,  Japan and Canada,  respectively.  For the three and  six-month  periods
ended December 31, 1998, due principally to the increasing product  contribution
from VIRACEPT  sales,  license fees and  royalties,  the Company  realized a net
income of $7,620,000 and $14,510,000.

RESULTS OF OPERATIONS

PRODUCT SALES

Product sales for the three and six-month  periods ended  December 31, 1998 were
approximately  $158,193,000  and  $292,063,000,  which  included  sales in North
America of $112,600,000 and $219,787,000,  respectively. The Company anticipates
that VIRACEPT sales in North America will meet or exceed  $440,000,000 in fiscal
1999.






                                       10



CONTRACT REVENUES

Collaborative  research  and  development  agreements  with Japan  Tobacco  Inc.
("JT"), Hoffmann-La Roche Inc. and F. Hoffmann-La Roche Ltd (collectively "HLR")
accounted for substantially all of the Company's contract revenues for the three
and six-month  periods ended December 31, 1998 and 1997. Total contract revenues
for the three and  six-month  periods  decreased  approximately  57% and 49% due
principally to termination of the HLR collaboration in fiscal 1998.

ROYALTIES AND LICENSE FEES

Royalty  revenues  of   approximately   $6,800,000  and  $11,725,000  have  been
recognized in the three and six-month  periods ended  December 31, 1998 based on
estimated  and  actual  Roche  sales  of  VIRACEPT  in its  licensed  territory.
Royalties  for the three and  six-month  periods  increased  from the prior year
periods due to growth in European market share and sales volume.

COST OF PRODUCT SALES

The  aggregate  cost of  product  sales as a  percentage  of  product  sales was
approximately 47% and 45% for the three and six-month periods ended December 31,
1998.  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 North America commercial sales were approximately 72% and
71% for the three and  six-month  periods ended  December 31, 1998.  The Company
anticipates  that gross margins on North America sales will  approximate 72% for
fiscal 1999.

RESEARCH AND DEVELOPMENT

Research and  development  spending for the current three and six-month  periods
increased  30% and 34%  from the  prior  year  periods  due  generally  to costs
associated with increasing average staff levels and staff related spending,  and
increasing expenses  associated with the clinical  development of certain of the
Company's anti-viral and anti-cancer compounds.

In fiscal 1997, the Company acquired Alanex  Corporation  ("Alanex",  a research
company) and recorded a write-off of $57,500,000  (or 92% of the purchase price,
including  transaction costs),  representing the values determined by management
to be attributable to the in-process technology purchased. Of the amount written
off, approximately 95% was attributed to and supported by a discounted cash flow
analysis of three drug discovery  programs which anticipated  revenues beginning
in 2003.  Approximately  40% of the  value was  attributed  to a  compound  with
obesity and  cardiovascular  indications,  30% for compounds with depression and
anxiety indications and 25% for a program to treat endometriosis and sex-hormone
dependent tumors. The Company believes that the allocations and aggregate values
attributable  to these  programs were  reasonable and  appropriate  based on the
commercial potential, beginning in 2003, of these three drug discovery programs,
which  remain the  subject of research or  development  efforts at December  31,
1998.

                                       11





SELLING, GENERAL AND ADMINISTRATIVE

Selling,  general and  administrative  costs for the current three and six-month
periods  increased by 47% and 42% from the prior year periods due principally to
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 three and six-month  periods ended December 31, 1998 and
represents  approximately 25% of North America product sales. Royalty expense in
the prior year periods was approximately 20% of North America product sales.

INCOME TAX PROVISION

The income tax  provision  in the  current  quarter has been  computed  using an
effective,  combined  federal and state rate of 15%. The cash obligation of such
provision has been mostly 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).

YEAR 2000

The Year 2000 issue results from computer programs and systems that were created
to accept only two digit dates. Such systems may not be able to distinguish 20th
century dates from 21st century dates. This could result in miscalculations  and
system  failures  that  could  inhibit a  company's  ability to engage in normal
business activities.

The  Company  has  established  a Year  2000  project  team and is  utilizing  a
multi-phased  approach  to  address  this  issue.  The  phases  included  in the
Company's   plan   are  the   awareness,   assessment,   remediation,   testing,
implementation,  and contingency  planning phases. The Company has completed the
awareness  and  assessment  phases and has begun to correct  and  replace  those
systems  that are not Year 2000  compliant.  The  Company  expects  to  complete
internal remediation efforts by the end of fiscal year 1999, and to complete the
validation and contingency phases by the end of calendar 1999.

The Company has initiated  communications  with all of its significant  external
business  partners to determine the extent to which the Company is vulnerable to
their  failures  and to ascertain  Year 2000  compliance  and risk.  The Company
intends to monitor the progress of these significant  business partners and will
develop  contingency  plans  in  the  event  that  a  significant   exposure  is
identified.  While the Company is not  presently  aware of any such  significant
exposure,  there can be no guarantee  that the systems of the  third-parties  on
which the  Company  relies  will be Year 2000  compliant,  or, that a failure to
remediate by another  company  would not have a material  adverse  effect on the
Company.

                                       12



The  Company  estimates  that the total cost of its Year 2000  project  will not
exceed $1,000,000, including costs already incurred. The anticipated cost of the
project and the dates on which the Company expects to complete major  milestones
are based on  management's  best estimates using  information  that is currently
available.  Based on its current estimates, the Company does not anticipate that
the costs  associated  with the Year 2000 project  will have a material  adverse
effect on the Company's business, financial position, or results of operation.

LIQUIDITY AND CAPITAL RESOURCES

Prior to fiscal 1998, the Company has relied  principally  on equity  financings
and corporate  collaborations  to fund its operations and capital  expenditures.
Beginning in fiscal 1998,  the gross  margin from  commercial  sales of VIRACEPT
contributed significantly to the Company's overall working capital requirements.
Commercial sales of VIRACEPT for the three and six-month  periods ended December
31,  1998  resulted  in  gross   margins  of   approximately   $83,952,000   and
$160,777,000.

At December  31,  1998,  the Company  had net working  capital of  approximately
$154,080,000,  an  increase  of  $26,352,000  over  June  30,  1998  levels  due
principally to the Company's  pre-tax  profit of  $17,071,000  and $9,825,000 in
proceeds  from  the  issuance  of  common  stock.   Individual  working  capital
components  significantly  impacted by the commercialization of VIRACEPT include
trade accounts receivable (an increase of $11,639,000), inventories (an increase
of  $713,000),   accounts  payable  (a  decrease  of  $19,535,000)  and  accrued
liabilities  (an  increase of  $8,221,000,  primarily  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  by
VIRACEPT sales. At December 31, 1998, the Company had cash, cash equivalents and
short-term investments of approximately  $73,734,000.  The Company believes that
its current capital resources,  existing contractual commitments and anticipated
VIRACEPT product sales are sufficient to maintain its current operations through
fiscal 1999. 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 after fiscal 1999 if significant and increasing positive
cash flows are not  generated  from  commercial  activities.  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  capabilities.  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,  cancel  licenses from third parties 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.

                  On January  27,  1999,  an action  entitled  Ruben v.  Agouron
                  Pharmaceuticals, Inc., et. al. was filed in San Diego Superior
                  Court against the Company,  members of its board of directors,
                  and Warner-Lambert  Company. The complaint,  which purports to
                  be  a  class   action   filed  on  behalf  of  the   Company's
                  shareholders, alleges that the board breached fiduciary duties
                  in  connection  with the decision to enter into the  Agreement
                  and  Plan  of  Merger  among  the  Company,   WLC  Acquisition
                  Corporation and  Warner-Lambert  Company,  dated as of January
                  26, 1999.  The  complaint  purports to seek  various  forms of
                  relief,  including  a  preliminary  and  permanent  injunction
                  against  consummation of the transaction  with  Warner-Lambert
                  Company  and/or  money  damages.   The  Company  believes  the
                  allegations are without merit.

ITEM 2.           Changes in Securities:  None

ITEM 3.           Defaults Upon Senior Securities:  None.


                                       14



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

                  The  Company  held  its  Annual  Meeting  of  Shareholders  on
                  December 16,  1998.  The  following  actions were taken at the
                  meeting:

                  1.     Shareholders  elected nine directors to serve until the
                         next annual meeting. Of the 31,282,508 shares of Common
                         Stock of the Company  outstanding as of the October 19,
                         1998   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
                                                                                        
                           Peter Johnson                     27,904,017                   127,489
                           Gary E. Friedman                  27,903,517                   127,989
                           John N. Abelson                   27,901,277                   130,229
                           Patricia M. Cloherty              27,602,377                   429,129
                           A. E. Cohen                       27,602,877                   428,629
                           Michael E. Herman                 27,607,127                   424,379
                           Irving S. Johnson                 27,605,663                   425,843
                           Antonie T. Knoppers               27,603,209                   428,297
                           Melvin I. Simon                   27,904,147                   127,359


                  2.     A  proposal  (the  "Divisional  Stock  Proposal")   was
                         approved.  The  proposal  approved  the  amendment  and
                         restatement of the Company's  Articles of Incorporation
                         to (i)  increase  the  number of  shares of  authorized
                         Common Stock to 150,000,000 shares, of which 75,000,000
                         shares  would   initially  be   designated  as  Agouron
                         Pharmaceuticals   Stock  and  25,000,000  shares  would
                         initially   be   designated   as   Oncology    Division
                         ("Oncoceutics")     Common    Stock,    (ii)    provide
                         authorization  to the Board to designate  and issue any
                         undesignated shares in one or more additional series of
                         Common  Stock,  to  determine  the  number  of  shares,
                         rights, preferences, privileges and restrictions of any
                         such series,  and to increase or decrease the number of
                         shares of any existing  series,  and (iii) convert each
                         share of the Company's  existing  Common Stock into one
                         share of Agouron  Pharmaceuticals  Stock and 0.5 shares
                         of Oncoceutics  Stock.  21,535,439 shares were voted in
                         favor of the  proposal,  5,530,848  shares  were  voted
                         against the  proposal,  138,535  shares  abstained  and
                         4,077,686   shares   were  not  voted  or  were  broker
                         non-votes.

                 3.      A proposal  to amend the  Company's  1996 Stock  Option
                         Plan to  increase  the number of shares  available  for
                         issuance  under  such  plan  by  1,000,000  shares  was
                         approved.  22,165,340 shares were voted in favor of the
                         proposal,  4,640,301  shares  were  voted  against  the
                         proposal,  399,181 shares  abstained and 826,684 shares
                         were not voted or were broker non-votes.


                                       15




                 4.      A  proposal  to  amend  the  Company's  Employee  Stock
                         Purchase   Plan  to  increase   the  number  of  shares
                         available  for  purchase  under  such  plan by  200,000
                         shares was  approved.  25,820,930  shares were voted in
                         favor of the  proposal,  1,020,130  shares  were  voted
                         against the  proposal,  363,762  shares  abstained  and
                         826,684 shares were not voted or were broker non-votes.

                 5.      The  selection  of  PricewaterhouseCoopers  LLP  as the
                         Company's   independent   accountants   was   ratified.
                         27,857,821  shares were voted in favor of the proposal,
                         66,419 shares were voted against the proposal,  107,266
                         shares  abstained  and 0 shares  were not voted or were
                         broker non-votes.

ITEM 5.           Other Information:  None

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

a.       Exhibits:
                      4.1(1)     Amended and Restated Rights Agreement dated
                                 as  of   November 10,  1998   between   Agouron
                                 Pharmaceuticals,     Inc.    and    ChaseMellon
                                 Shareholder Services, L.L.C.
                      10.1(2)    Amended and Restated 1996 Stock Option Plan.
                      10.2(2)    Amended and Restated Employee Stock Purchase
                                 Plan.
                      10.3(3)    Amended 1998 Employee Stock Option Plan.
                      10.4       Agreement  and  Plan  of  Merger  dated  as  of
                                 January 26, 1999 among Warner-Lambert  Company,
                                 WLC   Acquisition   Corporation   and   Agouron
                                 Pharmaceuticals, Inc.
                      10.5       Stock Option Agreement dated as of January 26,
                                 1999, by and between  Agouron  Pharmaceuticals,
                                 Inc. and Warner-Lambert Company.
                      10.6       Form of Employment Agreement dated January 26,
                                 1999 executed with Peter Johnson, Marvin R. 
                                 Brown,  Gary E. Friedman, Barry D. Quart and
                                 R. Kent Snyder (named executive officers in
                                 Proxy Statement dated November 12, 1998).
                      27.        Financial Data Schedule for the quarter ended
                                 December 31, 1998.

b.       Reports on Form 8-K:  None.

- ------------------
(1)      Incorporated by reference to Form 8-K filed January 19, 1999.
(2)      Incorporated by reference to Form S-4 filed August 13, 1998.
(3)      Incorporated by reference to Form S-8 filed January 19, 1999.


                                       16



                                    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:  February 5, 1999                    /s/ Steven S. Cowell
                                         ---------------------------------------
                                         Steven S. Cowell
                                         Corporate Vice President, Finance
                                         Chief Financial Officer
                                         Chief Accounting Officer


                                       17