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 MARCH 31, 1999


                         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 May 10,  1999,  the
registrant had  approximately  32,200,000  shares of Common Stock, no par value,
outstanding.

                                       1



                          AGOURON PHARMACEUTICALS, INC.

                                      INDEX


                                                                                          

                                                                                          PAGE NO.
                                                                                          --------

PART I.           Financial Information

ITEM 1.           Financial Statements

                  Consolidated Balance Sheet -                                                  3
                         March 31, 1999 and June 30, 1998

                  Consolidated Statement of Income -                                            4
                         Three and Nine Months Ended
                         March 31, 1999 and 1998

                  Consolidated Statement of Cash Flows-                                         5
                         Nine Months Ended March 31, 1999 and 1998

                  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                                                            15

ITEM 2.           Changes in Securities                                                        15

ITEM 3.           Defaults Upon Senior Securities                                              15

ITEM 4.           Submission of Matters to a Vote of Security Holders                          15

ITEM 5.           Other Information                                                            15

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

                  Signature                                                                    16


                                       2



PART I.       FINANCIAL INFORMATION


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



                                                                           March 31,               June 30,
                                                                                1999                   1998
                                                                      --------------         --------------
ASSETS                                                                   (unaudited)


                                                                                       
Current assets:
     Cash and cash equivalents                                        $       42,775         $      19,098
     Short-term investments                                                   41,692                68,025
     Accounts receivable, net                                                 58,334                51,341
     Inventories                                                              98,901               103,706
     Current deferred tax assets                                                 877                   564
     Other current assets                                                      2,580                 5,247
                                                                      --------------         -------------

     Total current assets                                                    245,159               247,981

Property and equipment, net of accumulated
     depreciation and amortization of $34,123 and $24,321                     48,066                47,212
Deferred tax assets                                                           71,262                64,644
Purchased intangibles                                                          3,050                 3,500
                                                                      --------------         -------------

                                                                      $      367,537         $     363,337
                                                                      ==============         =============
LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                                                 $       23,442         $      44,393
     Accrued liabilities                                                      50,183                35,356
     Deferred revenue and advances                                             8,101                23,563
     Current deferred tax liabilities                                          2,589                 1,139
     Loan payable and current portion of long-term debt                          857                15,802
                                                                      --------------         -------------

     Total current liabilities                                                85,172               120,253
                                                                      --------------         -------------

Long-term liabilities:
     Long-term debt, less current portion                                      6,170                 5,892
     Accrued rent                                                                822                 1,023
                                                                      --------------         -------------

     Total long-term liabilities                                               6,992                 6,915
                                                                      --------------         -------------

Stockholders' equity:
     Common stock, no par value, 75,000,000 shares authorized,
       32,070,124 and 31,053,380 shares issued and outstanding               373,377               348,482
     Accumulated other comprehensive income (expense)                           (727)                  384
     Accumulated deficit                                                     (97,277)             (112,697)
                                                                      --------------         -------------

     Total stockholders' equity                                              275,373               236,169
                                                                      --------------         -------------

                                                                      $      367,537         $     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             Nine Months Ended   
                                            ---------------------------    --------------------------
                                                      March 31,                     March 31,      
                                            ---------------------------    --------------------------  

                                                1999           1998            1999           1998   
                                            -----------     -----------    -----------    -----------

                                                                               
Revenues:
   Product sales                            $   145,993     $   111,950    $   438,056     $  283,252
   Contracts                                      5,877           8,608         17,310         31,073
   Royalties and license fees                     5,613          13,900         17,763         16,652
                                            -----------     -----------    -----------     ----------

                                                157,483         134,458        473,129        330,977
                                            -----------     -----------    -----------     ----------

Operating expenses:
   Cost of product sales                         60,268          49,220        191,554        121,235
   Research and development                      44,725          31,859        121,434         89,113
   Selling, general and administrative           23,411          14,168         61,254         40,759
   Royalties                                     29,027          18,081         83,005         46,889
                                            -----------     -----------    -----------     ----------

                                                157,431         113,328        457,247        297,996
                                            -----------     -----------    -----------     ----------

Operating income                                     52          21,130         15,882         32,981
                                            -----------     -----------    -----------     ----------

Other income (expenses):
   Interest and other income                      1,208           1,624          3,095          4,393
   Interest expense                                (190)           (212)          (836)          (579)
                                            -----------     -----------    -----------     ----------

                                                  1,018           1,412          2,259          3,814
                                            ------------    -----------    -----------     ----------

Income before income taxes                        1,070          22,542         18,141         36,795

Income tax provision                                160           9,017          2,721         14,718
                                            -----------     -----------    -----------     ----------

Net income                                  $       910     $    13,525    $    15,420     $   22,077
                                            ===========     ===========    ===========     ==========

Earnings per share:
      Basic                                 $       .03     $      .44     $       .49     $      .73
                                            ===========     ==========     ===========     ==========
      Diluted                               $       .03     $      .41     $       .45     $      .66
                                            ===========     ==========     ===========     ==========


Shares used in calculation of:
      Basic                                      31,936          30,757         31,491         30,414
      Diluted                                    35,291          32,956         34,236         33,251


See accompanying notes to consolidated financial statements.
                                       4




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




                                                                                         Nine Months Ended  
                                                                                  --------------------------
                                                                                             March 31,      
                                                                                  --------------------------
                                                                                      1999            1998  
                                                                                  ------------   -----------
                                                                                           
Cash flows from operating activities:
     Cash received from product sales, contracts, license fees
       and royalties                                                              $   450,674    $   311,174
     Cash paid to suppliers, employees and service providers                         (445,549)      (277,073)
     Interest received                                                                  3,084          4,443
     Interest paid                                                                       (836)          (579)
                                                                                  -----------    ------------

     Net cash provided (used) by operating activities                                   7,373         37,965
                                                                                  -----------    -----------

Cash flows from investing activities:
     Proceeds from maturities/sales of short-term investments                          51,619        102,113
     Purchases of short-term investments                                              (26,397)      (150,299)
     Purchases of property and equipment                                              (11,362)       (23,200)
                                                                                  -----------    -----------

     Net cash provided (used) by investing activities                                  13,860        (71,386)
                                                                                  -----------    -----------

Cash flows from financing activities:
     Net proceeds from issuance of common stock                                        17,111         11,411
     Proceeds from credit line                                                         40,000         22,600
     Principal payments on credit line, long-term debt,
      and capital leases                                                              (54,667)       (23,147)
                                                                                  -----------    -----------

     Net cash provided (used) by financing activities                                   2,444         10,864
                                                                                  -----------    -----------

Net increase (decrease) in cash and cash equivalents                                   23,677        (22,557)

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

Cash and cash equivalents at end of period                                        $    42,775    $    29,927
                                                                                  ===========    ===========

Reconciliation   of  net  income  to  net  cash  provided  (used)  by  operating
  activities:
     Net income                                                                   $    15,420    $    22,077
     Depreciation and amortization                                                     10,958          6,206
     Provision for deferred income taxes                                                2,303         14,282
     Net (increase) decrease in accounts receivable
       and other current assets                                                        (4,326)       (25,133)
     Net (increase) decrease in inventories                                             4,805        (32,200)
     Net increase (decrease) in accounts payable, accrued liabilities,
       deferred revenue and advances, and other liabilities                           (21,787)        52,733
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                             $     7,373    $    37,965
                                                                                  ===========    ===========

                                       

See accompanying notes to consolidated financial statements.

                                       5



                          AGOURON PHARMACEUTICALS, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                (March 31, 1999)


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
and Canada 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),  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.

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 confectionery  products.  Warner-Lambert  employs more
than 40,000 people worldwide.  The proposed merger, which is subject to approval
by  Agouron's  shareholders,  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 .8934 share of Warner-Lambert common stock.

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  March  31,  1999  and the  consolidated
statements of income and cash flows for the three and  nine-month  periods ended
March 31,  1999 and 1998 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
                                       6



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 Company recorded  approximately  $3,300,000 in  merger-related  costs in the
quarter   ended  March  31,  1999.  If  the  merger  is  approved  by  Agouron's
shareholders,  the  Company  expects  to  incur  an  additional  $11,300,000  in
merger-related costs in the quarter ended June 30, 1999.

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:



                                                                  March 31,          June 30,
         (Dollars in thousands)                                        1999             1998
                                                              -------------     ------------

                                                                                    
         Raw materials and work in process                    $      91,286     $      95,517
         Finished goods                                               7,615             8,189
                                                              -------------     -------------

                                                              $      98,901     $     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 nine-month  periods ended March
31, 1999 are  approximately  $31,488,000 and $103,764,000 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 nine-month  periods ended March 31, 1998, sales to
Roche were  approximately  $18,942,000 and  $30,362,000.  The Company receives a
royalty on Roche's subsequent commercial sales of such drug supplies.


                                       7



ROYALTIES AND LICENSE FEES

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

For the three and  nine-month  periods  ended  March 31,  1999,  the Company has
accrued and/or received  royalties of  approximately  $5,613,000 and $17,338,000
resulting  from  estimated  and actual net sales of VIRACEPT by Roche within its
licensed  territory.  For the three and nine-month periods ended March 31, 1998,
Roche royalties were approximately $1,900,000 and $2,652,000.

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   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 the
Company's 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 3,355,000 and 2,745,000 shares for the
three and nine-month periods ended March 31, 1999 were used to calculate diluted
earnings per share.  For the three and nine-month  periods ended March 31, 1998,
common stock  equivalents of  approximately  2,199,000 and 2,837,000 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.



                                       8



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
nine-month periods ended March 31, 1999, total comprehensive income was $344,000
and  $14,309,000,  respectively.  During the three and nine-month  periods ended
March 31, 1998, total comprehensive income was $13,525,000 and $22,077,000.

NOTE 3 - LITIGATION

In January  1999,  an action was filed on behalf of the  Company's  shareholders
against  the  Company,  members of its board of  directors,  and  Warner-Lambert
Company alleging that the board breached fiduciary duties in connection with the
decision to enter into an agreement to merge with  Warner-Lambert  Company.  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.

                                       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  nine-month  periods  ended March 31, 1999 and 1998 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 nine-month  periods
ended March 31, 1999, due  principally to the  increasing  product  contribution
from VIRACEPT  sales,  license fees and  royalties,  the Company  realized a net
income of $910,000 and  $15,420,000,  respectively.  Third quarter  results were
diluted  by  a  $5,000,000  milestone  fee  paid  to  IRC  in  conjunction  with
development  of REMUNE  and  approximately  $3,300,000  of costs  related to the
proposed merger with Warner-Lambert.

RESULTS OF OPERATIONS

PRODUCT SALES

Product  sales for the three and  nine-month  periods  ended March 31, 1999 were
approximately  $145,993,000  and  $438,056,000,  which  included  sales in North
America of $114,505,000 and $334,292,000,  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 nine-month  periods ended March 31, 1999 and 1998.  Total contract  revenues
for the three and nine-month  periods  decreased  approximately  32% and 44% due
principally to termination of the HLR collaboration in fiscal 1998.

ROYALTIES AND LICENSE FEES

Royalty  revenues  of   approximately   $5,613,000  and  $17,338,000  have  been
recognized  in the three and  nine-month  periods  ended March 31, 1999 based on
estimated  and  actual  Roche  sales  of  VIRACEPT  in its  licensed  territory.
Royalties for the three and nine-month periods increased from the prior year due
to growth in European market share and sales volume

License fee revenues of  $12,000,000  were  recognized in the prior year's three
month period when VIRACEPT was approved for marketing in Europe  (January  1998)
and Japan (March 1998).

COST OF PRODUCT SALES

The  aggregate  cost of  product  sales as a  percentage  of  product  sales was
approximately  41% and 44% for the three and nine-month  periods ended March 31,
1999.  The aggregate  cost of product sales as a percentage of product sales was
approximately  44% and 43% for the three and nine-month  periods ended March 31,
1998. Gross margins on North America commercial sales were approximately 73% and
72% for the three and  nine-month  periods  ended  March 31,  1999.  The Company
anticipates  that gross margins on North America sales will  approximate 73% for
fiscal 1999.

RESEARCH AND DEVELOPMENT

Research and development  spending for the current three and nine-month  periods
increased 40% and 36% from the prior year periods due to costs  associated  with
increasing average staff levels and staff related spending, a milestone fee paid
to IRC in  conjunction  with  development  of REMUNE,  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
 
                                      11



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  activities  at March 31,
1999.

SELLING, GENERAL AND ADMINISTRATIVE

Selling,  general and administrative  costs for the current three and nine-month
periods  increased by 65% and 50% from the prior year periods due principally to
increasing  sales and  marketing  activities,  the support of VIRACEPT  phase IV
marketing studies and costs related to the proposed merger with Warner-Lambert.

ROYALTIES

The  Company's  obligation  to share  VIRACEPT  profits  with JT is reflected in
royalty  expense for the three and  nine-month  periods ended March 31, 1999 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 has been computed using an effective,  combined federal
and state rate of 15%. This rate is expected to increase if the proposed  merger
with Warner-Lambert becomes effective during the fourth fiscal quarter. 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 the  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 and 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
                                       12



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.

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 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  nine-month  periods ended March
31,  1999  resulted  in  gross   margins  of   approximately   $85,725,000   and
$246,502,000.

At March  31,  1999,  the  Company  had net  working  capital  of  approximately
$159,987,000,  an  increase  of  $32,259,000  over  June  30,  1998  levels  due
principally to the Company's  pre-tax profit of $18,141,000  and  $17,111,000 of
proceeds  from  the  exercise  of  stock  options.  Individual  working  capital
components  significantly  impacted by the commercialization of VIRACEPT include
trade accounts  receivable (an increase of $4,660,000),  inventories (a decrease
of  $4,805,000),  accounts  payable (a  decrease  of  $20,951,000)  and  accrued
liabilities  (an increase of  $14,827,000,  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 March 31, 1999, the Company had cash,  cash  equivalents and
short-term investments of approximately  $84,467,000.  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.


                                       13



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.

                                       14



PART II. OTHER INFORMATION

ITEM 1.           Legal Proceedings:

                  On January  27,  1999,  an action  entitled  Rubin 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 parties have agreed,  with
                  approval of the court, that defendants' time to respond to the
                  complaint will be indefinitely extended and that such response
                  will not be due until 10 days after plaintiffs  request such a
                  response.  Agouron believes that the allegations  asserted are
                  without merit because,  among other things, they do not have a
                  basis in fact or in law.

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

ITEM 2.           Changes in Securities:  None

ITEM 3.           Defaults Upon Senior Securities:  None

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

ITEM 5.           Other Information:  None

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

                  a.       Exhibits:
                           27.  Financial  Data  Schedule for the quarter ended
                                March 31, 1999.

                  b.       Reports on Form 8-K:

                           A report on Form  8-K was filed on January 19,  1999,
                           reporting the amendment to the Company's  stockholder
                           rights plan.  A report on Form 8-K was also  filed on
                           January  28,  1999,  reporting  the  execution  of a 
                           definitive  agreement  to merge  with  Warner-Lambert
                           Company.

                                       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:  May 13, 1999             /s/ Steven S. Cowell                           
                               -------------------------------------------------
                               Steven S. Cowell
                               Corporate Vice President, Finance
                               Chief Financial Officer
                               Chief Accounting Officer