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, 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                          (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 April 10, 1998,  the
registrant had 30,866,764 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
                    March 31, 1998 and June 30, 1997

             Consolidated Statement of Income (Loss) -                       4
                    Three and Nine Months Ended
                    March 31, 1998 and 1997

             Consolidated Statement of Cash Flows-                           5
                    Nine Months Ended March 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            14

Item 5.      Other Information                                              14

Item 6.      Exhibits and Reports on Form 8-K                               14

             Signature                                                      15



                                       2




PART I.           FINANCIAL INFORMATION

Item 1.           Financial Statements

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



                                                                           March 31,               June 30,
                                                                                1998                  1997
ASSETS                                                                   (unaudited)
                                                                      --------------         -------------
                                                                                       
Current assets:
     Cash and cash equivalents                                        $       29,927         $      52,484
     Short-term investments                                                   87,019                38,833
     Accounts receivable, net                                                 55,940                31,375
     Inventories                                                              91,000                58,800
     Current deferred tax assets                                               1,654                   500
     Other current assets                                                      2,777                 2,209
                                                                      --------------         -------------

     Total current assets                                                    268,317               184,201

Property and equipment,  net of accumulated
     depreciation and amortization of $21,890 and $16,161                     40,998                22,613
Deferred tax assets                                                           52,011                56,000
Purchased intangibles                                                          3,650                 4,100
                                                                      --------------         -------------

                                                                      $      364,976         $     266,914
                                                                      ==============         =============
LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                                                 $       55,434         $      28,833
     Accrued liabilities                                                      30,401                 8,889
     Deferred revenue and advances                                            32,379                27,567
     Current deferred tax liabilities                                            154                   600
     Loan payable and current portion of long-term debt                        3,530                 2,526
                                                                      --------------         -------------

     Total current liabilities                                               121,898                68,415
                                                                      --------------         -------------

Long-term liabilities:
     Long-term debt, less current portion                                      5,330                 5,940
     Accrued rent                                                              1,085                 1,277
                                                                      --------------         -------------

     Total long-term liabilities                                               6,415                 7,217
                                                                      --------------         -------------

Stockholders' equity:
     Common stock, no par value, 75,000,000 shares authorized,
       30,854,475 and 29,429,920 shares issued and outstanding               340,437               317,133
     Accumulated deficit                                                    (103,774)             (125,851)
                                                                      --------------         -------------

     Total stockholders' equity                                              236,663               191,282
                                                                      --------------         -------------

                                                                      $      364,976         $     266,914
                                                                      ==============         =============


See accompanying notes to consolidated financial statements.


                                       3



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





                                                 Three Months Ended             Nine Months Ended
                                            ---------------------------    --------------------------
                                                      March 31,                     March 31,
                                            ---------------------------    --------------------------
                                                1998           1997            1998           1997
                                            -----------     -----------    -----------    -----------
                                                                                  
Revenues:
   Product sales                            $   111,950     $    13,401    $   283,252     $   13,401
   Contracts                                      8,608          16,212         31,073         48,835
   License fees and royalties                    13,900           9,000         16,652          9,000
                                            -----------     -----------    -----------     ----------

                                                134,458          38,613        330,977         71,236
                                            -----------     -----------    -----------     ----------

Operating expenses:
   Cost of product sales                         49,220           6,023        121,235          6,023
   Research and development                      31,859          28,431         89,113         81,367
   Selling, general and administrative           14,168          10,280         40,759         19,802
   Royalties                                     18,081               0         46,889              0
                                            -----------     -----------    -----------     ----------

                                                113,328          44,734        297,996        107,192
                                            -----------     -----------    -----------     ----------

Operating income (loss)                          21,130          (6,121)        32,981        (35,956)
                                            -----------     -----------    -----------     ----------

Other income (expense):
   Interest and other income                      1,624           1,441          4,393          4,965
   Interest expense                                (212)            (13)          (579)           (93)
                                            -----------     -----------    -----------     ----------

                                                  1,412           1,428          3,814          4,872
                                            -----------     -----------    -----------     ----------

Income (loss) before income taxes                22,542          (4,693)        36,795        (31,084)

Income tax provision                              9,017             306         14,718            918
                                            -----------     -----------    -----------     ----------

Net income (loss)                           $    13,525     $    (4,999)   $    22,077     $  (32,002)
                                            ===========     ===========    ===========     ==========

Earnings (loss) per share:
      Basic                                 $       .44     $     (.18)    $       .73     $    (1.21)
                                            ===========     ==========     ===========     ==========
      Diluted                               $       .41     $     (.18)    $       .66     $    (1.21)
                                            ===========     ===========    ===========     ==========


Shares used in calculation of:
      Basic                                      30,757          27,230         30,414         26,478
      Diluted                                    32,956          27,230         33,251         26,478


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,
                                                                                  --------------------------

                                                                                      1998           1997
                                                                                  -----------    -----------
                                                                                              
Cash flows from operating activities:
     Cash received from product sales, contracts, license fees
       and royalties                                                              $   311,174    $    51,422
     Cash paid to suppliers, employees and service providers                         (277,073)      (137,043)
     Interest received                                                                  4,443          4,965
     Interest paid                                                                       (579)           (93)
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                                  37,965        (80,749)
                                                                                  -----------    -----------

Cash flows from investing activities:
     Proceeds from maturities/sales of short-term investments                         102,113         82,898
     Purchases of short-term investments                                             (150,299)       (83,806)
     Purchases of property and equipment                                              (23,200)        (7,016)
                                                                                  -----------    -----------

     Net cash provided (used) by investing activities                                 (71,386)        (7,924)
                                                                                  -----------    -----------

Cash flows from financing activities:
     Net proceeds from issuance of common stock                                        11,411         80,271
     Proceeds from credit line                                                         22,600              0
     Principal payments on credit line, long-term debt,
      and capital leases                                                              (23,147)          (454)
                                                                                  ------------   ------------

     Net cash provided (used) by financing activities                                  10,864         79,817
                                                                                  -----------    -----------

Net increase (decrease) in cash and cash equivalents                                  (22,557)        (8,856)

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

Cash and cash equivalents at end of period                                        $    29,927    $     7,595
                                                                                  ===========    ===========

Reconciliation  of net income  (loss) to net cash  provided  (used) by operating
  activities:
     Net income (loss)                                                            $    22,077    $   (32,002)
     Depreciation and amortization                                                      6,206          2,475
     Provision for deferred income taxes                                               14,282              0
     Net (increase) decrease in accounts receivable
       and other current assets                                                       (25,133)       (12,721)
     Net (increase) decrease in inventories                                           (32,200)       (42,657)
     Net increase (decrease) in accounts payable, accrued liabilities,
       deferred revenue and advances, and other liabilities                            52,733          4,156
                                                                                  -----------    -----------

     Net cash provided (used) by operating activities                             $    37,965    $   (80,749)
                                                                                  ===========    ===========



See accompanying notes to consolidated financial statements.





                                       5




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


Note 1 - The Company and its significant accounting policies

The Company

Agouron Pharmaceuticals,  Inc. is an integrated pharmaceutical company committed
to the  discovery,  development,  manufacturing  and marketing of small molecule
drugs  engineered to inactivate  proteins which play key roles in cancer,  AIDS,
and other  serious  diseases.  The Company,  through its own sales and marketing
force, is currently marketing VIRACEPT(R) (nelfinavir mesylate), an HIV protease
inhibitor  which was cleared for  marketing  by the United  States Food and Drug
Administration  ("FDA") in March 1997. The Company intends to commercialize  any
subsequent  products through its own direct sales and marketing force in certain
markets or, when appropriate,  through manufacturing and marketing relationships
with other pharmaceutical companies.

Principles of consolidation

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

Financial statements and estimates

The  consolidated  balance  sheet as of  March  31,  1998  and the  consolidated
statements of income (loss) and cash flows for the three and nine-month  periods
ended  March 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, 1997 Annual Report on Form 10-K. Certain  information and
footnote  disclosures  normally  included in  financial  statements  prepared in
accordance with generally accepted accounting  principles have been condensed or
omitted   pursuant  to  the  Securities  and  Exchange   Commission   rules  and
regulations.  Interim results are not necessarily  indicative of results for the
full year.

The preparation of financial  statements in conformity  with generally  accepted
accounting principles requires management to make estimates and assumptions that
affect the reported  amounts of assets,  liabilities,  revenues and expenses and
related disclosures as of the date of the financial  statements.  Actual results
could differ from such estimates.

At March 31, 1998,  it has been assumed  that the existing  collaborations  with
Japan  Tobacco Inc.  ("JT") will  continue in  accordance  with their  agreement
terms.  As such,  approximately  $30,089,000  of cash  received from JT has been
classified as deferred contract revenue and advances.  Approximately $25,030,000
of the cash received from JT represents JT's advance




                                       6




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

In December 1997,  Agouron and Hoffmann-La  Roche Inc. and F. Hoffmann-La  Roche
Ltd  ("Roche")  agreed  to  end  their  anti-cancer   research  and  development
collaboration  which began in June 1996.  Agouron  has  regained  all  marketing
rights  to  its   anti-cancer   drugs   previously   within  the  scope  of  the
collaboration.  Included  in  deferred  contract  revenue  at March 31,  1998 is
approximately $1,821,000 of cash received from Roche which will be recognized as
contract revenue by the end of fiscal 1998.

Inventories

The inventories consist of the following components:

                                                March 31,          June 30,
                                                     1998              1997
                                            -------------     -------------

    Raw materials and work in process       $      85,428     $      57,883
    Finished goods                                  5,572               917
                                            -------------     -------------

                                            $      91,000     $      58,800
                                            =============     =============

Product sales

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

Also included in product sales for the three and nine-month  periods ended March
31, 1998 are  approximately  $18,942,000  and $30,362,000 of sales (at cost plus
contractually  determined  mark-ups)  to Roche of clinical and  commercial  drug
supplies to be used by Roche in its licensed territory.

License fees and royalties

License fees are  recognized  as revenue  when earned as generally  evidenced by
certain factors including:  receipt of such fees, the  non-refundable  nature of
such fees, and the  satisfaction of any performance  obligations.  In July 1997,
the Company and JT granted Roche certain exclusive rights to VIRACEPT in several
Asian  countries.  For such  rights,  the  Company  received  a  license  fee of
$2,000,000  from Roche.  In January  1998,  the European  Commission  authorized
VIRACEPT to be marketed in Europe. Upon such approval, the



                                       7




Company  recognized as revenue a license fee of $11,000,000 from Roche, which is
responsible  for the sales and  marketing of VIRACEPT in Europe.  In March 1998,
the Japanese Ministry of Health and Welfare  authorized  VIRACEPT to be marketed
in Japan. Upon such approval, the Company recognized as revenue a license fee of
$1,000,000  from Roche,  which is  responsible  for the sales and  marketing  of
VIRACEPT in several Asian territories including parts of Japan.

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

Income tax provision

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

Earnings (loss) per share

The  Company  computes  earnings  per  share in  accordance  with  Statement  of
Financial  Accounting  Standards No. 128  "Earnings  Per Share." Basic  earnings
(loss)  per share is based upon the  weighted  average  number of common  shares
outstanding during a period. Diluted earnings (loss) per share is based upon the
weighted  average number of common shares  outstanding and dilutive common stock
equivalents  during a period.  Common stock  equivalents  are options  under the
Company's  stock  option  plans  which are  included in the  earnings  per share
computation  under the treasury  stock method and common  shares  expected to be
issued under the Company's employee stock purchase plan.

Common stock equivalents of approximately 2,199,000 and 2,837,000 shares for the
three and nine-month periods ended March 31, 1998 were used to calculate diluted
earnings per share.  For the three and nine-month  periods ended March 31, 1997,
common stock  equivalents of  approximately  3,415,000 and 2,778,000 shares were
not used to  calculate  diluted  earnings  (loss)  per  share  because  of their
anti-dilutive  effect.  There  are  no  reconciling  items  in  calculating  the
numerator for basic and diluted earnings (loss) per share for any of the periods
presented.

Certain concentrations

A portion of the Company's research and development  expenditures are related to
programs  funded in whole or in part by corporate  partners.  The termination of
such collaborative research and development programs could result in the absence
of any prospective  funding for such programs and the need to evaluate the level
of future program spending, if any.





                                       8




Note 2 - Commitments

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


Note 3 - Stockholders' equity

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





                                       9




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

When used in this discussion,  the words  "believes,"  "anticipates" and similar
expressions are intended to identify forward-looking statements. Such statements
are subject to certain risks and uncertainties  (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, 1997 and incorporated herein by reference.  Readers are cautioned
not to place undue reliance on these forward-looking statements which speak only
as of the date hereof.  The Company undertakes no obligation to publicly release
the result of any  revisions to these  forward-looking  statements  which may be
made to reflect events or circumstances  after the date hereof or to reflect the
occurrence of unanticipated events.

Overview

The  Company is  committed  to the  discovery,  development,  manufacturing  and
marketing of human  pharmaceuticals  targeting  cancer,  AIDS, and other serious
diseases.  Operations  to date have been  principally  funded from the Company's
equity-derived  working capital,  various  collaborative  arrangements and, most
recently, from the gross margin contribution of its first product, VIRACEPT. The
net income  reported in the current three and nine-month  periods is principally
due to the commercialization of VIRACEPT while the Company's prior net operating
losses reflect primarily the result of its independent  research and substantial
investment in the clinical and  commercial  development  of VIRACEPT and certain
anti-cancer compounds.

In March 1997, the Company received  approval from the FDA to market VIRACEPT in
the United States. For the current three and nine-month periods, due principally
to the increasing  product  contribution  from VIRACEPT sales,  license fees and
royalties, the Company realized net income of $13,525,000 and $22,077,000.

Results of Operations

Product sales

Product sales for the current three and  nine-month  periods were  approximately
$111,950,000  and  $283,252,000,  which  included  sales in the United States of
$92,806,000  and  $252,688,000,   respectively.  The  Company  anticipates  that
VIRACEPT  sales  in  the  United  States  will   approximate   $350,000,000   to
$360,000,000 for fiscal 1998.

Contract revenues

Collaborative research and development agreements with Japan Tobacco Inc. ("JT")
and Roche accounted for substantially all of the Company's contract revenues for
the three and nine-month  periods ended March 31, 1998 and 1997.  Total contract
revenues for the three and nine-month  periods  decreased  approximately 47% and
36% due principally to decreased




                                       10





VIRACEPT  program  spending by Agouron,  which was  partially  funded by JT, and
increased  spending  by JT and  Roche on the  VIRACEPT  and  AG3340  development
programs, which was partially funded by Agouron.  Additionally, the amortization
to revenue over a 24 month period of JT's $24,000,000  milestone payment,  which
was received in August 1995, was completed in June 1997.

In December 1997, the Company agreed to end its collaboration  with Roche in the
field of cancer. As a result of the termination agreement,  Agouron has regained
all marketing rights to its anti-cancer drugs previously within the scope of the
Roche collaboration.  The Company does not foresee any significant impact on its
financial  results for the current  fiscal year due to  termination of the Roche
collaboration  since  a  substantial  portion  of the  anticipated  fiscal  1998
anti-cancer  research and development costs of such collaboration will have been
offset by contract  funding  received from Roche.  The Company  anticipates that
contract revenues for fiscal 1998 will approximate $40,000,000.

License fees and royalties

In January and March 1998,  VIRACEPT was  approved  for  marketing in Europe and
Japan,  respectively.  Upon such  approvals,  the Company  recognized as revenue
license fees totaling $12,000,000.

Royalty revenues of approximately $1,900,000 and $2,652,000 have been recognized
in the current three and nine-month  periods based on estimated and actual Roche
sales of VIRACEPT  in its  licensed  territory.  The  Company  anticipates  that
license fees and royalties for fiscal 1998 will approximate $20,000,000.

Cost of product sales

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 United States  commercial sales were  approximately  66%
during the current quarter and 63% for the nine months ended March 31, 1998. The
Company  anticipates  that gross margins on United States  commercial sales will
approximate 64% for fiscal 1998.

Research and development

Research  and  development  spending  increased  from the prior year periods due
generally to costs  associated  with  increasing  average staff levels and staff
related spending,  the acquisition of Alanex during the fourth quarter of fiscal
1997,  and  increasing  expenses  associated  with the clinical  development  of
certain of the Company's  anti-cancer  compounds.  The Company  anticipates that
total research and development expenses will approximate  $120,000,000 in fiscal
1998.

In  December  1997,  the  Company   discontinued   further  development  of  its
anti-cancer drug AG337 (THYMITAQ(TM),  nolatrexed  dihydrochloride) on the basis
of its interim  analysis of results from phase II/III  trials of the drug and in
order to concentrate available resources on




                                       11





the  development  of two  earlier-stage  anti-cancer  agents  that  the  Company
believes  have  greater  commercial  potential.  The Company  believes  that the
termination  of the THYMITAQ  development  program  will not have a  significant
impact on current year operating results.

Selling, general and administrative

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

Royalties

The  Company's  obligation  to share  VIRACEPT  profits  with JT is reflected in
royalty  expense for the current  three and  nine-month  periods and  represents
approximately 20% and 19% of United States product sales. It is anticipated that
royalty expense for the fourth quarter of fiscal 1998 will range from 20% to 21%
of United States 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 40%. 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).
The   Company's   accumulated   net  deferred  tax  assets  have   decreased  to
approximately $53,511,000 at March 31, 1998.

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. In
fiscal 1998,  due to the  successful  commercialization  of VIRACEPT,  operating
activities have provided  $37,965,000 of cash.  Commercial sales of VIRACEPT for
the three and  nine-months  ended  March 31, 1998  resulted in gross  margins of
approximately $62,730,000 and $162,017,000.

At March  31,  1998,  the  Company  had net  working  capital  of  approximately
$146,419,000,  an  increase  of  $30,633,000  over  June  30,  1997  levels  due
principally to the Company's pre-tax profit of $36,795,000.  Individual  working
capital components  significantly  impacted by the commercialization of VIRACEPT
include trade accounts receivable (an increase of $25,232,000),  inventories (an
increase of  $32,200,000),  accounts  payable (an increase of  $26,601,000)  and
accrued  liabilities  (an  increase  of  $21,512,000,  primarily  due to accrued
royalties  payable  to  JT).  It  is  anticipated  that  these  working  capital
components and cash and




                                       12




short-term  investments will continue to be  significantly  impacted as VIRACEPT
sales increase.  At March 31, 1998, the Company had cash,  cash  equivalents and
short-term investments of approximately $116,946,000.  The Company believes that
its current capital resources,  anticipated VIRACEPT product sales contribution,
existing   contractual   commitments  and  established   credit  facilities  are
sufficient to maintain its current  operations  through fiscal 1998. This belief
is based on current research and clinical development plans, anticipated working
capital  requirements   associated  with  the  expanding   commercialization  of
VIRACEPT, the current regulatory environment,  historical industry experience in
the development of therapeutic drugs and general economic conditions.

The Company believes that additional financing may be required to meet operating
needs beyond 1998 if its  commercial  activities  do not  generate  significant,
positive  operating  results on a consistent and timely basis or if the scope of
its  research,   development,   manufacturing   or   commercial   operations  is
substantially increased. Such needs would include the expenditure of substantial
funds to  continue  and expand  research  and  development  activities,  conduct
existing  and  planned  preclinical  studies  and human  clinical  trials and to
support the increasing  working  capital  requirements  of a growing  commercial
infrastructure  including  manufacturing,  sales and marketing. As a result, the
Company   anticipates   pursuing   various   financing   alternatives   such  as
collaborative arrangements and additional public offerings or private placements
of  securities.  If such  alternatives  are not  available,  the  Company may be
required to defer or restrict certain commercial activities,  delay or eliminate
expenditures  for certain of its  potential  products  under  development  or to
license third parties to commercialize products or technologies that the Company
would otherwise seek to develop or commercialize itself.




                                       13





PART II. OTHER INFORMATION

Item 1.           Legal Proceedings:

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

Item 2.           Changes in Securities:  None

Item 3.           Defaults Upon Senior Securities:  None

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

Item 5.           Other Information:  None

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

                    10.42  Form of 1998 Employee Stock Option Plan.

                    10.43* Form of 1998  Employee  Non-Statutory  Stock  Option
                           Agreement.

                    27.**  Financial  Data  Schedule for the quarter ended March
                           31, 1998.

                    27A.** Financial Data Schedule  (restated for the effect of
                           FAS128) for the quarter ended September 30, 1997.

                 b.  Reports on Form 8-K:  None








*  Incorporated by reference to Form S-8 dated February 19, 1998

** Exhibits 27 and 27A are submitted as exhibits only in the  electronic  format
   of this  Quarterly  Report on Form 10-Q submitted to the Securities and 
   Exchange Commission







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                                    SIGNATURE

Pursuant  to the  requirements  of the  Securities  Exchange  Act of  1934,  the
registrant  has duly  caused  this  report  to be  signed  on its  behalf by the
undersigned thereunto duly authorized.


                                        AGOURON PHARMACEUTICALS, INC.




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


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