<PAGE>   1
                                  UNITED STATES

                       SECURITIES AND EXCHANGE COMMISSION

                             Washington, D.C. 20549

                                   FORM 10-K/A
(Mark One)

[X]  ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934

                   FOR THE FISCAL YEAR ENDED DECEMBER 31, 1996

                                       OR

[ ]  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: 0-19707

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

                   DELAWARE                          87-0431168
        (State or other jurisdiction of           (I.R.S. Employer
        incorporation or organization)          Identification No.)

                    1244 Reamwood Avenue, Sunnyvale, CA 94089
          (Address of principal executive offices, including zip code)

       Registrant's telephone number, including area code: (408) 745-6010

        Securities registered pursuant to Section 12(b) of the Act: None

           Securities registered pursuant to Section 12(g) of the Act:
                     Common Stock, $0.01 par value per share


        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 by check mark if disclosure of delinquent filers pursuant to
Item 405 of Regulation S-K is not contained herein, and will not be contained,
to the best of registrant's knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K. [X]

        The aggregate market value of the voting stock held by non-affiliates of
the registrant was approximately $44,700,828 as of February 28, 1997, based upon
the closing sale price on the Nasdaq National Market reported for such date.
Shares of Common Stock held by each officer and director and by each person who
owns 5% of more of the outstanding Common Stock have been excluded in that such
persons may be deemed to be affiliates. This determination of affiliate status
is not necessarily a conclusive determination for other purposes.

        There were 21,618,658 shares of the registrant's Common Stock issued and
outstanding as of February 28, 1997.



<PAGE>   2



The Registrant hereby amends the following item of its Form 10-K for the fiscal
year ended December 31, 1996 filed with the Securities and Exchange Commission
on March 31, 1997 for the purpose of refiling Exhibit 10.34:

                                     PART IV

ITEM 14.  EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K

(a)     The following documents are filed as part of this Report:

        1.     Financial Statements and Schedules

               Financial Statements - See pages F-1 to F-16.

               Schedules not listed above have been omitted because they are not
               required or the information required to be set forth therein is
               included in the Financial Statements or notes thereto.

        2.     Exhibits

<TABLE>
<CAPTION>
               EXHIBIT
               NUMBER         DESCRIPTION
               <S>            <C>
               3.1(7)         Restated Certificate of Incorporation of Registrant.
               3.2(2)         Bylaws of Registrant.
               10.1*(4)       1987 Stock Option Plan, as amended.
               10.2*(8)       1991 Directors' Stock Option Plan, as amended.
               10.3*(8)       1991 Employee Stock Purchase Plan, as amended.
               10.4(1)        Purchase Agreement (Series C) dated as of June 26, 1990, as
                              amended.
               10.6(1)        Form of Indemnification Agreement between the Registrant and
                              its officers and directors.
               10.7*(1)       Defined Contribution "401(k)" Plan as amended January 1,  1990.
               10.8(1)        Equipment Financing Agreement dated as of June 1, 1990 between
                              Lease Management Services, Inc. and the Registrant
               10.9(2)        Lease dated June 1989 between the Registrant and William J.
                              Lowenberg.
               10.13*(3)      Letter Agreement with William G. Mavity.
               10.14*(4)      Consulting Agreement with Robert M. Curtis dated January 12,
                              1994.
               10.16(5)       Lease Extension with BSL Associates.
               10.17(5)       Lease Agreements with QAD Associates.
               10.18(5)(9)    Licensing Agreement with SENKO Medical Instrument Mfg. Co.,
                              Ltd.
               10.19*(5)      InnerDyne Medical, Inc. 1989 Incentive Stock Plan.
               10.20*(5)      Interventional Thermodynamics Inc. 401(k) Plan.
               10.22(6)(9)    License and Development Agreement dated as of August 25, 1994
                              by and among InnerDyne, Inc., InnerDyne Medical, Inc. and
                              CooperSurgical, Inc.
               10.23(7)       Loan and Security Agreement and Collateral
                              Assignment, Patent Mortgage and Security
                              Agreement dated as of February 23, 1995 between
                              the Registrant and Silicon Valley Bank.
               10.24(8)       Common Stock and Warrant Purchase Agreement
                              dated as of June 2, 1995 by and among the
                              Registrant and the purchasers named therein,
                              including form of Common Stock Warrant.
               10.25(10)      Amendment to Loan and Security Agreement dated
                              as of February 29, 1996 between the Registrant
                              and Silicon Valley Bank.
               10.26*(10)     1996 Stock Option Plan.
               10.27(9)(10)   Licensing, Development and Manufacturing
                              Agreement dated as of February 2, 1996 between
                              the Registrant and EndoTex Interventional
                              Systems, Inc.
               10.28(9)(10)   National Contract dated October 1995 between the Registrant
                              and Surgical
</TABLE>



                                      -2-
<PAGE>   3

<TABLE>
               <S>            <C>
                              Care Affiliates, Inc.
               10.29(9)(10)   License Agreement dated as of January 1, 1996
                              between the Registrant and Alliance of
                              Children's Hospitals, Inc.
               10.31*(10)     Letter Agreement with Robert A. Stern dated January 10, 1996.
               10.32*(11)     Change of Control Agreement dated as of September 12, 1996
                              between the Registrant and William G. Mavity.
               10.33+(11)     License Agreement dated as of December 20, 1996 by and among
                              the Registrant and United States Surgical Corporation.
               10.34+(11)(12) License, Supply and Distribution Agreement dated as of January
                              6, 1997 by and between the Registrant and
                              Sherwood Medical Company.
               10.35*(11)     Letter Agreement with Daniel J. Genter dated March 13, 1996.
               10.36(11)      Amendment to Loan and Security Agreement dated as of February
                              4, 1997 between the Registrant and Silicon Valley Bank.
               10.37*(11)     Form of Senior Management Change of Control Agreement.
               23.1(11)       Consent of Independent Certified Public Accountants.
               27.1(11)       Financial Data Schedule.
</TABLE>

               --------------
               *      Management compensatory plan or arrangement.
               +      Confidential treatment requested.

               (1) Incorporated by reference to exhibits filed in response to
               Item 16(a), "Exhibits," of the Registrant's Registration
               Statement on Form S-1, as amended (File No. 33-44361), filed
               December 4, 1991.

               (2) Incorporated by reference to exhibits filed in response to
               Item 14(a)(3), "Exhibits," of the Registrant's Annual Report on
               Form 10-K for the year ended December 31, 1992.

               (3) Incorporated by reference to exhibits filed in response to
               Item 6, "Exhibits and Reports on Form 8-K," of the Registrant's
               Quarterly Report on Form 10-Q for the quarterly period ended
               September 30, 1993.

               (4) Incorporated by reference to exhibits filed in response to
               Item 21, "Exhibits and Financial Statement Schedules," of the
               Registrant's Registration Statement on Form S-4, as amended (File
               No. 33-74624), filed January 31, 1994.

               (5) Incorporated by reference to exhibits filed in response to
               Item 6, "Exhibits and Reports on Form 8-K," of the Registrant's
               Quarterly Report on Form 10-QSB for the quarterly period ended
               June 30, 1994.

               (6) Incorporated by reference to exhibits filed in response to
               Item 6 "Exhibits and Reports on Form 8-K," of the Registrant's
               Quarterly Report on Form 10-QSB for the quarterly period ended
               September 30, 1994.

               (7) Incorporated by reference to exhibits filed in response to
               Item 13, "Exhibit List and Reports on Form 8-K," of the
               Registrant's Annual Report on Form 10-KSB for the year ended
               December 31, 1994.

               (8) Incorporated by reference to exhibits filed in response to
               Item 6, "Exhibits and Reports on Form 8-K" of the Registrant's
               Quarterly Report on Form 10-QSB for the quarterly period ended
               June 30, 1995.



                                      -3-
<PAGE>   4

               (9) Confidential treatment granted for portions of this exhibit
               by order of the Securities and Exchange Commission.

               (10) Incorporated by reference to exhibits filed in response to
               Item 13, "Exhibit List and Reports on Form 8-K," of the
               Registrant's Annual Report on Form 10-KSB for the year ended
               December 31, 1995.

               (11) Item filed as an exhibit to the Registrant's Annual Report
               on Form 10-K for the year ended December 31, 1996, to which this
               Form 10-K/A relates.

               (12) This exhibit reflects changes to certain redacted portions
               of this Agreement as compared to the version that was originally
               filed as an exhibit to the Registrant's Annual Report on Form
               10-K for the year ended December 31, 1996.

(b)     Reports on Form 8-K:  None










                                      -4-
<PAGE>   5



                                   SIGNATURES

        Pursuant to the requirements of Section 13 or 15(d) 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.



                                    INNERDYNE, INC.

Date: March 28, 1998                By:


                                    /s/ ROBERT A. STERN
                                    --------------------------------------------
                                    Robert A. Stern
                                    Vice President  and Chief Financial Officer
                                    (Principal Financial and Accounting Officer)










                                      -5-
<PAGE>   6


                                  EXHIBIT INDEX

<TABLE>
<CAPTION>
               EXHIBIT
               NUMBER         DESCRIPTION
               <S>            <C>
               3.1(7)         Restated Certificate of Incorporation of Registrant.
               3.2(2)         Bylaws of Registrant.
               10.1*(4)       1987 Stock Option Plan, as amended.
               10.2*(8)       1991 Directors' Stock Option Plan, as amended.
               10.3*(8)       1991 Employee Stock Purchase Plan, as amended.
               10.4(1)        Purchase Agreement (Series C) dated as of June 26, 1990, as
                              amended.
               10.6(1)        Form of Indemnification Agreement between the Registrant and
                              its officers and directors.
               10.7*(1)       Defined Contribution "401(k)" Plan as amended January 1,  1990.
               10.8(1)        Equipment Financing Agreement dated as of June 1, 1990 between
                              Lease Management Services, Inc. and the Registrant
               10.9(2)        Lease dated June 1989 between the Registrant and William J.
                              Lowenberg.
               10.13*(3)      Letter Agreement with William G. Mavity.
               10.14*(4)      Consulting Agreement with Robert M. Curtis dated January 12,
                              1994.
               10.16(5)       Lease Extension with BSL Associates.
               10.17(5)       Lease Agreements with QAD Associates.
               10.18(5)(9)    Licensing Agreement with SENKO Medical Instrument Mfg. Co.,
                              Ltd.
               10.19*(5)      InnerDyne Medical, Inc. 1989 Incentive Stock Plan.
               10.20*(5)      Interventional Thermodynamics Inc. 401(k) Plan.
               10.22(6)(9)    License and Development Agreement dated as of August 25, 1994
                              by and among InnerDyne, Inc., InnerDyne Medical, Inc. and
                              CooperSurgical, Inc.
               10.23(7)       Loan and Security Agreement and Collateral
                              Assignment, Patent Mortgage and Security
                              Agreement dated as of February 23, 1995 between
                              the Registrant and Silicon Valley Bank.
               10.24(8)       Common Stock and Warrant Purchase Agreement
                              dated as of June 2, 1995 by and among the
                              Registrant and the purchasers named therein,
                              including form of Common Stock Warrant.
               10.25(10)      Amendment to Loan and Security Agreement dated
                              as of February 29, 1996 between the Registrant
                              and Silicon Valley Bank.
               10.26*(10)     1996 Stock Option Plan.
               10.27(9)(10)   Licensing, Development and Manufacturing
                              Agreement dated as of February 2, 1996 between
                              the Registrant and EndoTex Interventional
                              Systems, Inc.
               10.28(9)(10)   National Contract dated October 1995 between the Registrant
                              and Surgical


</TABLE>



<PAGE>   7

<TABLE>

               <S>            <C>
                              Care Affiliates, Inc.
               10.29(9)(10)   License Agreement dated as of January 1, 1996
                              between the Registrant and Alliance of
                              Children's Hospitals, Inc.
               10.31*(10)     Letter Agreement with Robert A. Stern dated January 10, 1996.
               10.32*(11)     Change of Control Agreement dated as of September 12, 1996
                              between the Registrant and William G. Mavity.
               10.33+(11)     License Agreement dated as of December 20, 1996 by and among
                              the Registrant and United States Surgical Corporation.
               10.34+(11)(12) License, Supply and Distribution Agreement dated as of January
                              6, 1997 by and between the Registrant and
                              Sherwood Medical Company.
               10.35*(11)     Letter Agreement with Daniel J. Genter dated March 13, 1996.
               10.36(11)      Amendment to Loan and Security Agreement dated as of February
                              4, 1997 between the Registrant and Silicon Valley Bank.
               10.37*(11)     Form of Senior Management Change of Control Agreement.
               23.1(11)       Consent of Independent Certified Public Accountants.
               27.1(11)       Financial Data Schedule.
</TABLE>

               --------------
               *      Management compensatory plan or arrangement.
               +      Confidential treatment requested.

               (1) Incorporated by reference to exhibits filed in response to
               Item 16(a), "Exhibits," of the Registrant's Registration
               Statement on Form S-1, as amended (File No. 33-44361), filed
               December 4, 1991.

               (2) Incorporated by reference to exhibits filed in response to
               Item 14(a)(3), "Exhibits," of the Registrant's Annual Report on
               Form 10-K for the year ended December 31, 1992.

               (3) Incorporated by reference to exhibits filed in response to
               Item 6, "Exhibits and Reports on Form 8-K," of the Registrant's
               Quarterly Report on Form 10-Q for the quarterly period ended
               September 30, 1993.

               (4) Incorporated by reference to exhibits filed in response to
               Item 21, "Exhibits and Financial Statement Schedules," of the
               Registrant's Registration Statement on Form S-4, as amended (File
               No. 33-74624), filed January 31, 1994.

               (5) Incorporated by reference to exhibits filed in response to
               Item 6, "Exhibits and Reports on Form 8-K," of the Registrant's
               Quarterly Report on Form 10-QSB for the quarterly period ended
               June 30, 1994.

               (6) Incorporated by reference to exhibits filed in response to
               Item 6 "Exhibits and Reports on Form 8-K," of the Registrant's
               Quarterly Report on Form 10-QSB for the quarterly period ended
               September 30, 1994.

               (7) Incorporated by reference to exhibits filed in response to
               Item 13, "Exhibit List and Reports on Form 8-K," of the
               Registrant's Annual Report on Form 10-KSB for the year ended
               December 31, 1994.

               (8) Incorporated by reference to exhibits filed in response to
               Item 6, "Exhibits and Reports on Form 8-K" of the Registrant's
               Quarterly Report on Form 10-QSB for the quarterly period ended
               June 30, 1995.




<PAGE>   8

               (9) Confidential treatment granted for portions of this exhibit
               by order of the Securities and Exchange Commission.

               (10) Incorporated by reference to exhibits filed in response to
               Item 13, "Exhibit List and Reports on Form 8-K," of the
               Registrant's Annual Report on Form 10-KSB for the year ended
               December 31, 1995.

               (11) Item filed as an exhibit to the Registrant's Annual Report
               on Form 10-K for the year ended December 31, 1996, to which this
               Form 10-K/A relates.

               (12) This exhibit reflects changes to certain redacted portions
               of this Agreement as compared to the version that was originally
               filed as an exhibit to the Registrant's Annual Report on Form
               10-K for the year ended December 31, 1996.