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                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   FORM 10-Q/A


|X|      AMENDMENT TO QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
         SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED JUNE 30,
         1996.

| |      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 0-19955


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

        Delaware                                   94-3050031
        (State or other jurisdiction               (IRS Employer Identification
        of incorporation or organization)          Number)



               928 EAST ARQUES AVENUE, SUNNYVALE, CALIFORNIA 94086
              (Address of principal executive offices and zip code)

                                 (408) 773-1222
              (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.


                                                      |X| Yes          | |  No
         As of July 28, 1996, 10,208,356 shares of Common Stock of the
Registrant were outstanding.
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                  The Undersigned Registrant hereby amends Part II, Items 1 and
6 of its Quarterly Report on Form 10-Q for the quarter ended June 30, 1996, as
set forth below:


PART II. OTHER INFORMATION

Item 1:  Legal Proceedings.

         Molecular Dynamics, Inc. (the "Company") entered into a settlement
agreement dated March 20, 1996 with Meridian Instruments, Inc. ("Meridian") with
respect to the litigation initiated by the Company at the United States District
Court for the Northern District of California on December 14, 1994, Molecular
Dynamics, Inc. v. Meridian Instruments, Inc., Civil Action No. C 94-4292 SAW
(JSB) ENE, alleging that Meridian is infringing United States Patent Re. 34,214
("Patent 34,214") relating to three-dimensional images generated from confocal
microscope systems. The settlement provides for a mutual release of all claims
and counterclaims in the suit between the parties and dismissal of the case, a
grant to Meridian of a non-exclusive license under Patent 34,214 and related
patents and a grant of certain rights to shares of Meridian stock ("Shares").
The Company does not believe that disclosure of the amount or the attributed
value of the Shares would be meaningful since Meridian is a private company and
there is no current public market for the Shares. In addition, the Company
cannot exercise any rights relating to the Shares until certain conditions are
met. The Company accounted for the Shares on a cost basis and their attributed
value is immaterial. As of this date, Meridian has paid no dividend on the
Shares, nor does the Company anticipate that Meridian will pay a dividend on the
Shares in the foreseeable future.

         On April 11, 1996, the Company filed a complaint against Leica, Inc.
for patent infringement in the United States District Court for the Northern
District of California, Molecular Dynamics, Inc. v. Leica Inc., Civil Action No.
C 96-20280 RMW (PVT). The complaint seeks injunctive relief and damages for the
infringement of Patent 34,214. The Company seeks its lost profits due to the
defendants' infringement of the patent, and a permanent injunction to stop the
infringing acts.

Item 6:  Exhibits and Reports on Form 8-K

         (a)      Exhibit 10.38 - Settlement Agreement by and between Molecular
                  Dynamics, Inc. and Meridian Instruments, Inc., dated as of
                  March 20, 1996.

         (b)      Exhibit 11.1 - Statement re Computation of Earnings Per Share

         (c)      There were no reports on Form 8-K during the quarter ended
                  June 30, 1996.


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                                  EXHIBIT INDEX
      


      Exhibit No.                    Document

         10.38*      Settlement Agreement by and between Molecular Dynamics,
                      Inc. and Meridian Instruments, Inc., dated as of March 20,
                      1996.

         11.1(1)     Statement re Computation of Earnings Per Share

         ------- 
         "*" on such exhibits indicates that portions have been omitted
         for which confidential treatment has been requested and filed
         separately with the Securities and Exchange Commission.


         (1) Incorporated by reference from an identically numbered exhibit
         filed with the Company's Quarterly Report on Form 10-Q (File No.
         0-19955) filed with the Securities and Exchange Commission on August
         13, 1996

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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, in Sunnyvale, California on this 10th
day of January, 1997.


                                    MOLECULAR DYNAMICS, INC.



                                    By:     /s/ JAY FLATLEY
                                            -----------------------------------
                                            Jay Flatley
                                            President, Chief Executive Officer,
                                            Chief Operating Officer, Acting
                                            Chief Financial Officer and Member
                                            of the Board of Directors


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