<PAGE>   1
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549





                                    Form 10-Q


(Mark one)

    X      Quarterly report pursuant to Section 13 or 15(d) of the Securities 
  -----    Exchange Act of 1934.  For the quarterly period ended March 31, 1997.

  -----    Transition report pursuant to Section 13 or 15(d) of the Securities 
           Exchange Act of 1934.  For the transition period
           from                                          to             .
                ----------------------------------------    ------------

                             Commission File Number
                                     0-19290


                             COR THERAPEUTICS, INC.
             (Exact name of registrant as specified in its charter)

            Delaware                                      94-3060271
(State or other jurisdiction of                        (I.R.S. employer
incorporation or organization)                        identification no.)


          256 East Grand Avenue, South San Francisco, California 94080
              (Address of principal executive offices and zip code)

                                 (415) 244-6800
              (Registrant's telephone number, including area code)

         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.

         Common Stock $.0001 par value                 20,078,484
                                                       ----------
                                                 Outstanding at April 30, 1997

                                       1
<PAGE>   2
                             COR THERAPEUTICS, INC.





                                      INDEX
<TABLE>
<CAPTION>
                                                                        PAGE NO.
                                                                        ------- 
<S>          <C>                                                          <C> 
PART I.       FINANCIAL INFORMATION                                     

Item 1.       Financial Statements and Notes

 
              Condensed Balance Sheets - March 31, 1997
              and December 31, 1996                                         3

              Statements of Operations - for the three months
              ended March 31, 1997 and 1996                                 4

              Statements of Cash Flows - for the three months
              months ended March 31, 1997 and 1996                          5

              Notes to Financial Statements                                 6

Item 2.       Management's Discussion and Analysis of Financial Condition
              and Results of Operations                                     6

PART II.      OTHER INFORMATION

Item 6.       Exhibits and Reports on Form 8-K                              9

SIGNATURES                                                                  9

COR(TM) and INTEGRILIN(TM) are trademarks of the Company.
</TABLE>


                                       2
<PAGE>   3
                             COR THERAPEUTICS, INC.
                                 BALANCE SHEETS
                                 (in thousands)
<TABLE>
<CAPTION>
                                     ASSETS

                                                                 March 31,          December 31,
                                                              -------------        -------------
                                                                  1997                 1996
                                                              -------------        -------------
                                                               (Unaudited)
<S>                                                          <C>                  <C>           
Current assets:
     Cash and cash equivalents                               $        8,658       $        2,615
     Short-term investments                                          37,774               50,519
     Contract receivables                                             7,369                7,644
     Other current assets                                             3,263                3,420
                                                              -------------        -------------
         Total current assets                                        57,064               64,198

Property and equipment, net                                           6,613                7,047
                                                              -------------        -------------
                                                              $      63,677        $      71,245
                                                              =============        =============


                              LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
     Accounts payable                                        $        2,958       $        1,398
     Accrued compensation                                             1,967                1,495
     Accrued development costs                                        6,254                7,830
     Deferred revenue                                                 2,300                2,900
     Other accrued liabilities                                        1,174                  994
     Long-term debt--current portion                                  1,013                1,157
     Capital lease obligations--current portion                       1,713                1,664
                                                              -------------        -------------
         Total current liabilities                                   17,379               17,438
Long-term debt--noncurrent portion                                      482                  644
Capital lease obligations--noncurrent portion                         2,854                2,721

Stockholders' equity:                                               178,695              178,500
     Accumulated deficit                                           (135,733)            (128,058)
                                                              -------------        -------------
         Total stockholders' equity                                  42,962               50,442
                                                              -------------        -------------
                                                              $      63,677        $      71,245
                                                              =============        =============
</TABLE>



                                       
                             See accompanying notes.

                                       3
<PAGE>   4
                             COR THERAPEUTICS, INC.
                            STATEMENTS OF OPERATIONS
                    (in thousands, except per share amounts)
                                   (Unaudited)
<TABLE>
<CAPTION>
                                                                   Three Months Ended
                                                                        March 31,
                                                     -----------------------------------------------
                                                           1997                       1996
                                                     --------------------        -------------------

<S>                                                  <C>                       <C>                  
Contract revenues                                    $              6,325       $              2,531

Expenses:
     Research and development                                      12,033                     13,141
     Marketing, general and administrative                          2,505                      1,812
                                                     --------------------        -------------------
             Total expenses                                        14,538                     14,953
                                                     --------------------        -------------------

Loss from operations                                               (8,213)                   (12,422)

Interest income                                                       709                      1,126
Interest expense                                                     (171)                      (194)
                                                     --------------------        -------------------

Net loss                                             $             (7,675)       $           (11,490)
                                                     ====================        ===================

Net loss per share                                   $              (0.38)       $             (0.59)
                                                     ====================        ===================

Shares used in computing net loss per share                        20,040                     19,464
                                                     ====================        ===================
</TABLE>


















                             See accompanying notes.


                                       4
<PAGE>   5
                                                                  
                             COR THERAPEUTICS, INC.
                            STATEMENTS OF CASH FLOWS
                Increase (decrease) in cash and cash equivalents
                                 (in thousands)
                                  (Unaudited)




<TABLE>
<CAPTION>
                                                                           Three Months Ended
                                                                                March 31,
                                                                      ----------------------------
                                                                          1997             1996
                                                                      -----------      -----------
<S>                                                                  <C>               <C>       
Cash flows provided by (used in) operating activities:
  Net loss                                                           $    (7,675)      $  (11,490)
  Adjustments to reconcile net loss to net
   cash used in operating activities:
      Depreciation and amortization                                          933            1,059
      Amortization of deferred compensation                                   46               39
      Changes in assets and liabilities:
        Other current assets                                                 432             (933)
        Accounts payable                                                   1,560              108
        Accrued compensation                                                 600             (368)
        Accrued development costs                                         (1,576)            (804)
        Deferred revenue                                                    (600)               --
        Other accrued liabilities                                            180             (287)
                                                                     -----------      -----------
          Total adjustments                                                1,575           (1,186)
                                                                     -----------      -----------
          Net cash used in operating activities                           (6,100)         (12,676)
                                                                     -----------      -----------
Cash flows provided by (used in) investing activities:
  Purchases of short-term investments                                     (3,704)          (2,533)
  Sales of short-term investments                                         13,317           10,777
  Maturities of short-term investments                                     3,000            4,000
  Additions to property and equipment                                       (499)          (1,296)
                                                                     -----------      -----------
          Net cash provided by investing activities                       12,114           10,948
                                                                     -----------      -----------
Cash flows provided by (used in) financing activities:
  Principal payments on long-term debt                                      (306)            (316)
  Proceeds from capital lease obligations                                    572              326
  Principal payments under capital lease obligations                        (391)            (259)
  Issuance of common stock                                                   154              169
                                                                     -----------      -----------
          Net cash provided by (used in) financing activities                 29              (80)
                                                                     -----------      -----------
Net increase (decrease) in cash and cash equivalents                       6,043           (1,808)
Cash and cash equivalents at the beginning of the period                   2,615            5,463
                                                                     -----------      -----------
Cash and cash equivalents at the end of the period                   $     8,658      $     3,655
                                                                     ===========      ===========
</TABLE>


                            See accompanying notes.



                                       5
<PAGE>   6
                             COR THERAPEUTICS, INC.

                                                         
NOTES TO FINANCIAL STATEMENTS

1. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

COR Therapeutics, Inc. (the "Company") was incorporated in Delaware on February
4, 1988. The Company is focused on the discovery, development and
commercialization of novel pharmaceutical products for the treatment and
prevention of severe cardiovascular diseases.

Interim financial information

The accompanying unaudited condensed financial statements have been prepared in
accordance with generally accepted accounting principles for interim financial
information and with the instructions for Form 10-Q and Article 10 of Regulation
S-X. In the Company's opinion, the financial statements include all adjustments,
consisting only of normal recurring adjustments, which the Company considers
necessary to fairly state the Company's financial position and the results of
operations and cash flows. The balance sheet at December 31, 1996 has been
derived from the audited financial statements at that date but does not include
all of the information and footnotes required by generally accepted accounting
principles for complete financial statements. The accompanying financial
statements should be read in conjunction with the financial statements and notes
thereto included in the Company's Annual Report on Form 10-K for the year ended
December 31, 1996. The results of the Company's operations for any interim
period are not necessarily indicative of the results of the Company's operations
for any other interim period or for a full fiscal year.

2. EARNINGS PER SHARE

In February 1997, the Financial Accounting Standards Board issued Statement No.
128, Earnings per Share, which is required to be adopted on December 31, 1997.
At that time, the Company will be required to change the method currently used
to compute earnings per share and to restate all prior periods. Under the new
requirements for calculating primary earnings per share, the dilutive effect of
stock options will be excluded. The impact of Statement 128 is expected to
result in no change to the Company's primary net loss per share for the quarters
ended March 31, 1997 and 1996, as the antidilutive effect of stock options has
been excluded from the current computation. The impact of Statement 128 on the
calculation of the Company's fully-diluted earnings per share for these quarters
is not expected to be material.

Item 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF
         FINANCIAL CONDITION AND RESULTS OF OPERATIONS

OVERVIEW


This document includes forward-looking statements which involve risks and
uncertainties. Actual results of the Company's activities may differ
significantly from the potential results discussed in such forward-looking
statements. Risk factors that might cause such differences include, but are not
limited to, those factors identified below and under the captions "Business" and
"Additional Risk Factors" in the Company's Annual Report on Form 10-K for fiscal
1996. The Company's business is subject to significant risks including, but not
limited to, the success of its research and development efforts, the lengthy and
expensive regulatory process, possible competition from other products and
obtaining and enforcing patents important to the Company's business. Even if the
Company's potential products appear promising at various stages of development,
they may not reach the market for a number of reasons. Such reasons include, but
are not limited to, the
                                       6
<PAGE>   7
                             COR THERAPEUTICS, INC.

possibilities that the potential products will be found ineffective during
clinical trials, fail to receive necessary regulatory approvals, be difficult to
manufacture on a large scale, be uneconomical to market or be precluded from
commercialization by proprietary rights of third parties. Additional expenses,
delays and losses of opportunities that may arise out of these and other risks
could have a material adverse impact on the Company's financial condition and
results of operations.

Since its inception, COR has focused on the discovery, development and
commercialization of novel pharmaceutical products for the treatment and
prevention of severe cardiovascular diseases. The Company has not generated any
product revenues. The Company has been unprofitable since inception and has
incurred a cumulative net loss of $135,733,000 during the period from inception
to March 31, 1997. The Company's principal sources of working capital have been
primarily public equity financings and proceeds from collaboration research and
development agreements, as well as private equity financings, grant revenues,
interest income and property and equipment financings.

The Company's most advanced product in clinical development is INTEGRILIN(TM)
(antithrombotic injection). The Company submitted a New Drug Application ("NDA")
to the United States Food and Drug Administration (the "FDA") seeking approval
to market the INTEGRILIN(TM) product for use in helping to prevent acute cardiac
ischemic complications in patients undergoing percutaneous transluminal coronary
angioplasty ("PTCA"). INTEGRILIN(TM) was studied in this setting in IMPACT II, a
large, multi-center Phase III clinical trial. In February 1997, the FDA's
Cardiovascular and Renal Drugs Advisory Committee (the "Committee") considered
the Company's filing in PTCA. The Committee concluded that the IMPACT II trial
of INTEGRILIN(TM) had shown positive results as an adjunct therapy in helping to
prevent acute cardiac ischemic complications in patients undergoing PTCA.
However, because the Committee also decided that the results of the IMPACT II
trial alone were not sufficient to forego the FDA's customary requirement of two
positive clinical trials prior to the approval of a new drug, the Committee
recommended against approval of INTEGRILIN(TM) at this time.

In March 1997, the Company received an action letter from the FDA
regarding the NDA. The not-approvable letter identified clinical and technical
issues that need to be resolved, including the FDA's conclusion that IMPACT II
was not sufficiently robust as a single study to support approval. In its
letter, the FDA noted that a study in unstable angina is ongoing and that the
data should be provided which may add support to the findings of the IMPACT II
study. In March 1997, the Company notified the FDA of the Company's intention
to file an amendment addressing the issues cited. An amendment to the NDA would
need to include data from PURSUIT, a Phase III trial of INTEGRILIN(TM) for use
in connection with unstable angina/non-Q wave myocardial infarction. Enrollment
in the PURSUIT trial was completed in January 1997 and data are expected to be
available later in 1997. In April 1997, the Company announced the withdrawal of
the application made by its worldwide partner for INTEGRILIN(TM),
Schering-Plough ("Schering"), to the European Agency for the Evaluation of
Medicinal Products, the central regulatory agency for several European
countries, for European marketing approval of INTEGRILIN(TM). There can be no
assurance that INTEGRILIN(TM) or any of the Company's other products in
development will receive marketing approval in any country on a timely basis or
at all. If the Company is unable to demonstrate the safety or efficacy of
INTEGRILIN(TM) to the satisfaction of the FDA or other regulatory authorities,
the Company's business, financial condition and results of operations would be
materially adversely affected.

In addition to its collaboration agreement with Schering-Plough, the Company has
collaboration agreements with Ortho Pharmaceutical Corporation ("Ortho"), a
subsidiary of Johnson & Johnson, and Kyowa Hakko Kogyo Co., Ltd. In late 1996,
the Company and Ortho extended the collaboration agreement for one or two years.




                                       7
<PAGE>   8
                             COR THERAPEUTICS, INC.


RESULTS OF OPERATIONS

Contract revenues for the quarter ended March 31, 1997 increased 150% as
compared to the corresponding period in 1996, primarily due to receipt in 1997
of a milestone payment of $3,000,000 related to the completion of enrollment in
the PURSUIT trial, as well as the timing of recognition of contract revenues
under the Company's collaborative agreements with Schering and Ortho.

Research and development expenses decreased 8% for the quarter ended March 31,
1997 as compared to the corresponding period in 1996 primarily due to the timing
of costs associated with the PURSUIT trial. The Company expects research and
development expenses to increase over the next several years, although the
timing of certain of these expenses may depend on the timing and phase of, and
indications pursued in, clinical trials of potential products.

Marketing, general and administrative expenses increased by 38% for the quarter
ended March 31, 1997, as compared to the corresponding period in 1996, primarily
due to pre-commercial activities associated with INTEGRILIN(TM) (antithrombotic
injection), as well as increases in staffing and administrative expenses related
to general corporate activities. The Company expects marketing, general and
administrative expenses to continue to increase significantly over the next
several years.

Interest income decreased by 37% for the quarter ended March 31, 1997, as
compared to the corresponding period in 1996, primarily due to lower cash and
investment balances. Interest expense decreased 12% for the quarter ended March
31, 1997, as compared to the corresponding period of 1996, reflecting the
decrease in the average balance of debt outstanding.

The results of the Company's operations for any interim period are not
necessarily indicative of the results of the Company's operations for any other
interim period or for a full fiscal year.

LIQUIDITY AND CAPITAL RESOURCES

The Company has funded its operations primarily through public equity financings
and proceeds from collaboration research and development agreements, as well as
private equity financings, grant revenues, interest income and property and
equipment financings. The Company had available cash, cash equivalents and
short-term investments of $46,432,000 at March 31, 1997. Cash in excess of
immediate requirements is invested according to the Company's investment policy,
which provides guidelines with regard to liquidity and return and, wherever
possible, seeks to minimize the potential effects of concentration and credit
risk.

The Company expects that its cash requirements may increase in future years due
to costs related to continuation and expansion of research and development,
including clinical trials, and increased marketing, general and administrative
activities. The Company anticipates that its existing capital resources and
interest earned thereon will enable it to maintain its current and planned
operations at least into 1998. However, the Company's capital requirements may
change depending on numerous factors, including, but not limited to, the
progress of the Company's research and development programs, the scope and
results of preclinical and clinical studies, the number and nature of the
indications the Company pursues in clinical studies, the timing of regulatory
approvals, technological advances, determinations as to the commercial potential
of the Company's products and the status of competitive products. In addition,
expenditures will be dependent on existing and the establishment of new,
collaborative relationships with other companies, the availability of financing
and other factors. The Company will need to raise substantial additional funds
in the future, and there can be no assurance that such funds will be available
on favorable terms, if at all. In such event, the Company may need to delay or
curtail its research and development activities to a significant extent.

                                       8
<PAGE>   9
                             COR THERAPEUTICS, INC.


PART II.  OTHER INFORMATION

Item 6.  Exhibits and Reports on Form 8-K

         (a)  Exhibits
<TABLE>
<S>            <C>    <C>      <C>
                *      10.26    Registrant's 1994 Non-employee Directors'
                                Stock Options Plan, as amended.
                *      10.30    Registrant's 1991 Equity Incentive Plan, as amended.
                       27.1     Financial Data Schedule.

         (b)  Reports
                       There were no reports on Form 8-K filed for the quarter
                       ended March 31, 1997.
</TABLE>
-----------------------------------
         * Indicates management contracts or compensatory plans or arrangements
filed pursuant to Item 601(b)(10) of Regulation S-K.


                                   SIGNATURES

         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.


Date:    May 14, 1997

COR THERAPEUTICS, INC.


By: /s/ VAUGHN M. KAILIAN                     By:  /s/ LAURA A. BREGE
    ---------------------                          ---------------------------
    Vaughn M. Kailian                         Laura A. Brege
    President and Chief Executive Officer     Vice President, Finance and
                                              Chief Financial Officer

                                              By:  /s/ PETER S. RODDY
                                                   ---------------------------
                                              Peter S. Roddy
                                              Director, Finance and Controller

                                       9





<PAGE>   10
                                 EXHIBIT INDEX

<TABLE>
<CAPTION>

Exhibit #        Description
---------        -----------
<S>             <C>

10.26           Registrant's 1994 Non-employee Director's Stock Options Plan,
                as amended.

10.30           Registrant's 1991 Equity Incentive Plan, as amended.

27.1            Financial Data Schedule.
</TABLE>