<PAGE>
                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C. 20549
                                       
                                   FORM 10-Q
                                       
                                       

[X]  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 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 0-19955
                                                     -------


                           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 October 26, 1997, 10,351,426 shares of Common Stock of the Registrant 
were outstanding.

                                       1
<PAGE>

                           MOLECULAR DYNAMICS, INC.
                                       
                                     INDEX
                                       
                                       
                                       
                        PART I.  FINANCIAL INFORMATION
                                       

<TABLE>
<CAPTION>

Item 1.   Financial Statements                                                   Page(s)
                                                                                 -------
<S>                                                                            <C>
          Condensed Consolidated Balance Sheets
          September 30, 1997 and December 31, 1996...............................   3

          Condensed Consolidated Statements of Income
          Three and nine months ended September 30, 1997 and 1996................   4

          Condensed Consolidated Statements of Cash Flows
          Nine months ended September 30, 1997 and 1996..........................   5

          Notes to Interim Condensed Consolidated Financial Statements...........   6-7

Item 2.   Management's Discussion and Analysis of
          Financial Condition and Results of Operations..........................   8-11


PART II.  OTHER INFORMATION


Item 6.   Exhibits and Reports on Form 8-K.......................................   12

Signatures.......................................................................   13

</TABLE>

                                       2
<PAGE>


PART I.   FINANCIAL INFORMATION

ITEM 1.   FINANCIAL STATEMENTS
                                       
                   MOLECULAR DYNAMICS, INC. AND SUBSIDIARIES
                     CONDENSED CONSOLIDATED BALANCE SHEETS
                       (IN THOUSANDS, EXCEPT SHARE DATA)
                                       
                                                     SEPTEMBER 30,  DECEMBER 31,
                                                         1997           1996
                                                         ----           ----
                                                     (Unaudited)
ASSETS

Current assets:
 Cash and cash equivalents                             $  10,957       $  8,024
 Securities available-for-sale                            11,404         12,617
 Trade accounts receivable, net                           11,927         11,002
 Other accounts receivable                                 4,299          1,559
 Inventories                                               9,445          6,869
 Prepaids and other current assets                           579            347
                                                       ---------       --------
  Total current assets                                    48,611         40,418

Property and equipment, net                                4,654          2,997
Other assets, net                                          2,772          2,628
                                                       ---------       --------

  Total assets                                         $  56,037       $ 46,043
                                                       ---------       --------
                                                       ---------       --------
LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
 Accounts payable                                      $   4,407       $  3,264
 Accrued expenses                                          4,512          5,073
 Factoring liability                                         644          1,124
 Unearned revenue and customer advances                    5,840          3,068
                                                       ---------       --------
  Total current liabilities                               15,403         12,529
                                                       ---------       --------

Stockholders' equity:
 Common stock and additional paid-in capital              39,247         39,964
 Retained earnings (deficit)                               1,543         (2,425)
 Cumulative translation adjustment                          (165)           (88)
 Unrealized gain on securities available-for-sale              9              5
 Less 0 and 445,800 shares of common
  stock in treasury in 1997 and 1996,
  respectively, at cost                                        -         (3,943)
                                                       ---------       --------

  Total stockholders' equity                              40,634         33,514
                                                       ---------       --------

  Total liabilities and stockholders' equity           $  56,037       $ 46,043
                                                       ---------       --------
                                                       ---------       --------
SEE ACCOMPANYING NOTES.

                                       3
<PAGE>

                                       
                                       
                   MOLECULAR DYNAMICS, INC. AND SUBSIDIARIES
                  CONDENSED CONSOLIDATED STATEMENTS OF INCOME
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
                                  (UNAUDITED)

<TABLE>
<CAPTION>

                                                            THREE MONTHS ENDED            NINE MONTHS ENDED
                                                               SEPTEMBER 30,                 SEPTEMBER 30,
                                                            1997           1996           1997           1996
                                                            ----           ----           ----           ----
<S>                                                   <C>            <C>           <C>             <C>
Sales and other revenue                                 $  14,368      $  12,910      $  41,254      $  35,945
Cost of sales and other revenue                             6,607          5,800         18,303         15,741
                                                        ---------      ---------      ---------      ---------

  Gross profit                                              7,731          7,110         22,951         20,204
                                                        ---------      ---------      ---------      ---------

Operating expenses:
 Research and development                                   1,519          1,513          5,203          4,859
 Sales and marketing                                        3,654          3,615         10,539         11,078
 General and administrative                                 1,294            975          3,492          2,661
                                                        ---------      ---------      ---------      ---------

  Total operating expenses                                  6,467          6,103         19,234         18,598
                                                        ---------      ---------      ---------      ---------

  Operating income                                          1,294          1,007          3,717          1,606

Interest income, net                                          273            212            790            583
Other income                                                   (4)           (12)             2             16
                                                        ---------      ---------      ---------      ---------

  Income before income taxes                                1,563          1,207          4,509          2,205

Income taxes                                                  188            139            541            220
                                                        ---------      ---------      ---------      ---------

  Net income                                            $   1,375      $   1,068      $   3,968      $   1,985
                                                        ---------      ---------      ---------      ---------
                                                        ---------      ---------      ---------      ---------

Earnings per share                                      $     .12      $     .10      $     .35      $     .19
                                                        ---------      ---------      ---------      ---------
                                                        ---------      ---------      ---------      ---------

Shares used to compute earnings per share                  11,535         10,629         11,274         10,668
                                                        ---------      ---------      ---------      ---------
                                                        ---------      ---------      ---------      ---------
</TABLE>


SEE ACCOMPANYING NOTES.

                                       4
<PAGE>


                   MOLECULAR DYNAMICS, INC. AND SUBSIDIARIES
                CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                (IN THOUSANDS)
                                  (UNAUDITED)
                                                                 
                                                            NINE MONTHS ENDED
                                                              SEPTEMBER 30,
                                                              -------------
                                                           1997           1996
                                                           ----           ----
CASH FLOWS FROM OPERATING ACTIVITIES:
  Net cash provided by operating activities                2,010          3,918
                                                        --------       --------

CASH FLOWS FROM INVESTING ACTIVITIES:
 Purchases of property and equipment                      (2,699)          (944)
 Capitalized software development costs                     (568)          (360)
 Purchases of securities available-for-sale              (30,631)       (14,842)
 Maturities and sales of securities available-for-sale    31,852         16,997
 Other assets                                                (98)           (69)
                                                        --------       --------
  Net cash (used in) provided by investing activities     (2,144)           782
                                                        --------       --------

CASH FLOWS FROM FINANCING ACTIVITIES:
 Proceeds from employee stock purchase plans
  and option exercises                                       921              -
 Purchase of treasury stock                                    -         (1,519)
 Reissuance of treasury stock                              2,303            976
 Net decrease in factoring liability                        (480)             -
                                                        --------       --------
  Net cash provided by (used in) financing activities      2,744           (543)
                                                        --------       --------

Effect of exchange rate changes on cash                      323            241
                                                        --------       --------
Net increase in cash and cash equivalents                  2,933          4,398
Cash and cash equivalents at beginning of period           8,024          2,727
                                                        --------       --------

CASH AND CASH EQUIVALENTS AT END OF PERIOD              $ 10,957       $  7,125
                                                        --------       --------
                                                        --------       --------

SEE ACCOMPANYING NOTES.

                                       5
<PAGE>

                                       
                   MOLECULAR DYNAMICS, INC. AND SUBSIDIARIES
                                       
                                       
         NOTES TO INTERIM CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                  (UNAUDITED)
                                       
                                       
NOTE 1 - BASIS OF PRESENTATION

  The accompanying condensed consolidated balance sheets of Molecular 
Dynamics, Inc. and subsidiaries (Molecular Dynamics or the Company) as of 
September 30, 1997 and December 31, 1996 and the related condensed 
consolidated statements of operations for the three and nine month periods 
ended September 30, 1997 and 1996 and condensed consolidated statements of 
cash flows for the nine months ended September 30, 1997 and 1996 have been 
prepared on substantially the same basis as are the annual consolidated 
financial statements.  In the opinion of management, the financial statements 
reflect all adjustments, consisting only of normal recurring adjustments, 
necessary for a fair presentation of the financial position, operating 
results and cash flows for those periods presented.  The results of 
operations for the three and nine months ended September 30, 1997 are not 
necessarily indicative of results to be expected for the entire year.  These 
condensed consolidated financial statements should be read in conjunction 
with the consolidated financial statements, and notes thereto, for the year 
ended December 31, 1996 included in the Company's Form 10-K/A.

  For clarity of presentation the Company has indicated that its third 
quarters ended September 30 and its fiscal year ended December 31, whereas in 
fact, the Company's third quarters for fiscal years 1997 and 1996 ended on 
September 28, 1997 and September 29, 1996, respectively, and its fiscal year 
ended December 29, 1996.

NOTE 2 - INVENTORIES

  Inventories consisted of (in thousands):
                                                   September 30,   December 31,
                                                       1997           1996
                                                       ----           ----

       Raw material                                 $  4,905       $  3,045
       Work-in-process                                 2,534          1,786
       Finished goods                                  2,006          2,038
                                                    --------       --------
                                                    $  9,445       $  6,869
                                                    --------       --------
                                                    --------       --------

NOTE 3 - NEW ACCOUNTING STANDARDS

  In February 1997, the Financial Accounting Standards Board issued Statement 
of Financial Accounting Standards No. 128 "Earnings Per Share" (SFAS No.128), 
which requires the presentation of basic earnings per share (EPS) and, for 
companies with complex capital structures, diluted EPS.  SFAS No. 128 is 
effective for annual and interim periods ending after December 15, 1997; 
earlier application is not permitted.  The Company expects that basic EPS 
will be higher than primary earnings per share as presented in the 
accompanying consolidated financial statements, although the two amounts may 
round to the same number.  The Company has not yet analyzed how the 
calculation of diluted earnings per share will compare to primary or fully 
diluted earnings per share amounts. All prior period earnings per share 
amounts will be restated upon adoption.


                                       6
<PAGE>

NOTE 4. - COLLABORATION WITH AFFYMETRIX, INC.

In the third quarter of 1994, a consortium led by Affymetrix, Inc. and the 
Company was awarded funding from the Advanced Technology Program of the 
National  Institute of Standards and Technology (NIST).  The Company and its 
partner, Affymetrix, collaborate with researchers at several academic and 
research institutions in an effort to develop miniaturized DNA diagnostic 
systems.  The two companies will receive up to $31 million in matching funds 
to be divided approximately 33% to the Company and 67% to Affymetrix over the 
five years of the grant beginning in January 1995, for research and 
development in the field of DNA diagnostic devices with a total shared 
project cost of $63 million.  Approximately $12 million of the $31 million 
was available for the first two years of the grant period, which ended in 
January 1997. The Company has received notification from NIST that funding 
has been authorized for the remaining term of the grant, which ends in 
January 2000. The additional funding will allow the Company to work toward 
developing new fluorescence detection technologies and DNA separation devices 
and apply these to the expanding field of molecular genetics. In the third 
quarter and first nine months of 1997, the Company reduced research and 
development expenses by approximately $392,000 and $1.8 million, 
respectively, representing support from the grant, compared to $449,000 and 
$1.4 million, respectively, in the prior year periods.  In addition, in the 
third quarter and first nine months of 1997, the Company reduced its 
capitalized software by approximately $118,000 and $366,000, respectively, 
compared to $74,000 and $233,000 in the prior year periods, respectively, 
representing support from the grant.

NOTE 5. - STOCK REPURCHASE PROGRAM

In May 1994, the Board of Directors authorized the purchase of up to 
1,000,000 shares of the Company's common stock in the open market, and in 
February 1997 the Board increased this amount by 500,000 shares.  The Company 
has purchased approximately 1,000,000 shares under this program as of 
September 30, 1997.  Of these, approximately 1,000,000 shares were reissued 
under the Company's Stock Option and Employee Stock Purchase Plans, of which 
approximately 446,000 shares were reissued during the first nine months of 
1997.

NOTE 6. - TECHNOLOGY ACCESS PROGRAM

The Company and Amersham Life Science Ltd. are developing systems for 
fluorescence analysis of DNA in microarrays.  The two companies are pursuing 
agreements with genomics, pharmaceutical and biotechnology companies to 
provide them with microarray systems prior to their release to the general 
market, in exchange for funding and collaborative expertise.  In November 
1996, the Company entered into one agreement for early access to this 
technology.  During the first nine months of 1997, the companies entered into 
six additional agreements.  Subsequent to September 28,1997 one additional 
agreement has been signed.  Research and development expenses for the third 
quarter and first nine months of 1997 were reduced by $566,000 and $799,000, 
respectively, of credits representing amortization of fees from clients 
participating in the Company's technology access program.


                                       7
<PAGE>

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

  The following discussion should be read in conjunction with the attached 
condensed consolidated financial statements and notes thereto, and with the 
Company's audited financial statements and notes thereto for the fiscal year 
ended December 31, 1996.

  EXCEPT FOR THE HISTORICAL INFORMATION CONTAINED HEREIN, THE MATTERS 
DISCUSSED IN THIS DOCUMENT ARE FORWARD-LOOKING STATEMENTS THAT INVOLVE 
CERTAIN RISKS AND UNCERTAINTIES, INCLUDING THE RISKS AND UNCERTAINTIES SET 
FORTH BELOW UNDER "FACTORS THAT MAY AFFECT FUTURE RESULTS".  SUCH FORWARD 
LOOKING STATEMENTS ARE BASED ON CURRENT EXPECTATIONS AND ACTUAL RESULTS MAY 
DIFFER MATERIALLY.

RESULTS OF OPERATIONS

SALES AND OTHER REVENUE.  The Company's third quarter 1997 sales and other 
revenue of $14.4 million increased 11.3% from sales and other revenue of 
$12.9 million in the third quarter of 1996.  This increase resulted primarily 
from increases in sales of the Company's MegaBACE-TM- 1000 high-throughput 
sequencing instruments to test-site customers and recognition of revenue 
pursuant to agreements for early access to systems and technology for the 
analysis of DNA in microarrays, partially offset by decreases in sales of its 
scanner product line.  Additionally, sales and other revenue for the nine 
months ended September 30, 1997 were $41.3 million, an increase of 14.8% from 
sales and other revenue of $35.9 million in the comparable prior year period. 
This increase resulted from increases in sales of the MegaBACE-TM- 1000 
high-throughput sequencing instruments to test-site customers, recognition of 
revenue pursuant to agreements for early access to systems and technology for 
the analysis of DNA in microarrays and increases in sales of its scanner 
product line.  The Company sells its products through direct sales operations 
in North America, the United Kingdom, Germany, France, Japan and Australia.  
Changes in foreign currency exchange rates had the effect of decreasing the 
Company's sales and other revenue by approximately $957,000 for the nine 
months ended September 30, 1997 compared to the prior-year period.  Foreign 
currency fluctuations for the third quarter of 1997 had the effect of 
decreasing the Company's sales and other revenue by approximately $345,000 
compared to the prior year period.

GROSS MARGINS.  Gross margins for the third quarter and first nine months of 
1997 were 54.0% and 55.6%, respectively, compared to 55.1% and 56.2% in each 
of the respective prior year periods. The decrease in gross margins between 
the third quarters is primarily due to increased sales of lower-margin 
instruments and pre-production microarray systems compared to total sales.  
Although similar factors impacted the comparable nine-month periods, such 
factors were offset by the technology access fees associated with the 
Company's technology access program for microarray systems, with no 
associated cost of revenue.

RESEARCH AND DEVELOPMENT.  Research and development expenses for the third 
quarter and first nine months of 1997 were $1.5 and $5.2 million, 
respectively, compared to $1.5 and $4.9 million in the respective prior year 
periods.  The increase in the first nine months of 1997 compared to the prior 
year period resulted from the expansion of major development programs, offset 
by credits to expense representing recognition of fees from clients 
participating in the Company's program for early access to technology for the 
analysis of DNA in microarrays, and a slight increase in support from the 
Company's NIST Grant. Research and development expenses decreased as a 
percentage of sales and other revenue to 10.6% and 12.6% in the third quarter 
and first nine months of 1997, respectively, compared to 11.7% and 13.5% in 
the third quarter and first nine months of 1997, respectively, primarily due 
to the increase in sales and other revenue between the 

                                       8
<PAGE>

two periods.  Research and development expenses for the third quarter and 
first nine months of 1997 were reduced by $392,000 and $1.8 million, 
respectively, of credits representing support from the Company's NIST grant, 
compared to $449,000 and $1.4 million, respectively, of credits in the prior 
year periods.  Research and development expenses for the third quarter and 
first nine months of 1997 were also reduced by $566,000 and $799,000, 
respectively, of credits representing amortization of fees from clients 
participating in the Company's technology access program.  In addition, in 
the third quarter and first nine months of 1997, the Company reduced its 
capitalized software by approximately $118,000 and $366,000, respectively, 
representing support from the grant, compared to $95,000 and $360,000, 
respectively, for the comparable prior-year periods.

SALES AND MARKETING.  Sales and marketing expenses for the third quarter and 
first nine months of 1997 were $3.7 and $10.5 million as compared to $3.6 and 
$11.1 million in the respective prior year periods. The decrease between the 
nine-month periods is primarily the result of improved resource allocations 
within the Company's sales and marketing departments, changes in foreign 
currency rates and improved efficiency.  As a percentage of sales and other 
revenues, sales and marketing expenses decreased to 25.4% and 25.5% for the 
third quarter and first nine months of 1997, respectively, from 28.0% and 
30.8% in the respective prior year periods, due primarily to the increase in 
sales and other revenues.  Changes in foreign currency exchange rates had the 
effect of decreasing the Company's sales and marketing expenses by 
approximately $348,000 for the first nine months of 1997 compared to the 
prior-year period. Foreign currency fluctuations for the third quarter of 
1997 had the effect of decreasing the Company's sales and marketing expenses 
by approximately $106,000 compared to the prior year period.

GENERAL AND ADMINISTRATIVE.  General and administrative expenses for the 
third quarter and first nine months of 1997 were $1.3 million and $3.5 
million, as compared to $1.0 million and $2.7 million in the respective prior 
periods.  As a percentage of revenue, general and administrative expenses 
increased to 9.0% and 8.5% for the third quarter and first nine months of 
1997, respectively, from 7.6% and 7.4% in the respective prior periods.  
These increases were primarily due to legal expenses associated with patent 
and general litigation issues, not completely offset by increases in sales 
and other revenues.

PROVISION FOR INCOME TAXES.  During the third quarter and first nine months 
of 1997, the Company recorded tax expense utilizing an annual effective tax 
rate of 12.0% as compared to a rate of 10.0% for the third quarter and first 
nine months of 1996.  The increased tax rates in 1997 are attributable to the 
anticipated complete utilization of federal and several state net operating 
loss carryovers during 1997, resulting in federal Alternative Minimum Taxes 
and state regular taxes, while the low tax rates in 1996 are attributable to 
usage of net operating loss carryovers, and consist of state and federal 
Alternative Minimum Taxes.  The Company has remaining federal and state tax 
credits available to offset future regular federal and state income tax 
liabilities.

EARNINGS PER SHARE.   The Company generated earnings per share of $.12 and 
$.35, respectively, in the third quarter and first nine months of 1997 as 
compared to earnings per share of $.10 and $.19 in the respective comparable 
periods of 1996.  This improvement is due primarily to the increase in sales 
and other revenue and expense controls.  Weighted average shares outstanding 
used in computing earnings per share were 11.5 and 11.3 million shares for 
the third quarter and first nine months of 1997, respectively, as compared to 
10.6 and 10.7 million shares for the comparable periods in 1996

FACTORS THAT MAY AFFECT FUTURE RESULTS

                                       9
<PAGE>

The Company believes that results of operations in any quarterly period may 
be impacted by factors such as delays in the introduction or shipment of new 
products, in the timing of the signing of agreements for early access to 
technology, the timing of the recognition of fees from such agreements, 
difficulty in acquiring critical product components of acceptable quality and 
in required quantity, the effect of announcements of new competitive 
products, increases in legal expenses, increased competition, changes in the 
Company's product mix, a slower growth rate in the Company's target markets, 
order deferrals in anticipation of new product releases, or lack of market 
acceptance of new products, reduction or delay of government and private 
sector funding of research activities, or adverse changes in economic 
conditions in any of the countries in which the Company does business.  Also, 
during periods when a significant portion of net sales and net income are 
contributed by international operations, fluctuations of the U.S. dollar 
against foreign currencies such as those that have occurred in the past could 
affect the Company's results of operations and financial condition in a 
particular quarter.  There can be no assurance that the Company will be able 
to grow in future periods or continue profitability on a quarterly basis.

Due to the factors noted above, the Company's future earnings and stock price 
may be subject to significant volatility, particularly on a quarterly basis. 
Any shortfall in revenues or earnings from levels expected by securities 
analysts could have an immediate and significant adverse effect on the 
trading price of the Company's common stock.  The Company typically 
recognizes a substantial portion of sales near the end of a quarter.  
Therefore, the Company may not become aware of such shortfalls until late in 
a quarter, which may result in an adverse effect on the trading price of the 
Company's common stock.

LIQUIDITY AND CAPITAL RESOURCES

Working capital as of September 30, 1997 was $33.2 million, compared to $27.9 
million at December 31, 1996.  During the first nine months of this fiscal 
year, the issuance of treasury stock for employee stock option and purchase 
plans was the source of approximately $2.3 million of working capital, and 
working capital was used to purchase approximately $2.7 million in fixed 
assets, primarily related to expansion of the Company's facilities.

The Company's principal commitments at September 30, 1997 consisted of 
obligations under operating leases for facilities and equipment.  Long term 
cash requirements, other than normal operating expenses, are anticipated for 
development of new products, enhancement of existing products, financing 
continued growth, and possible acquisition of products, technologies or 
businesses complementary to the Company's business.  The Company believes its 
cash, securities available-for-sale, and cash flows from operating activities 
will be sufficient to satisfy its working capital requirements for the 
foreseeable future.

NEW ACCOUNTING STANDARDS.  In February 1997, the Financial Accounting 
Standards Board issued Statement of Financial Accounting Standards No. 128 
"Earnings Per Share" (SFAS No.128), which requires the presentation of basic 
earnings per share (EPS) and, for companies with complex capital structures, 
diluted EPS. SFAS No. 128 is effective for annual and interim periods ending 
after December 15, 1997; earlier application is not permitted.  The Company 
expects that basic EPS will be higher than primary earnings per share as 
presented in the accompanying consolidated financial statements, although the 
two amounts may round to the same number.  The Company has not yet analyzed 
how the calculation of diluted earnings per share will compare to primary or 
fully diluted earnings per share amounts. All prior period earnings per share 
amounts will be restated upon adoption.

In June 1997, the Financial Accounting Standards Board issued Statement of 
Financial Accounting Standards No. 130 "Reporting Comprehensive Income" (SFAS 
130) which will be effective for financial statements for periods beginning 
after December 15, 1997, and establishes standards for reporting and 

                                       10
<PAGE>

display of comprehensive income and its components in a full set of general 
purpose financial statements. Earlier application is permitted.  The Company 
will make the required reporting of comprehensive income in its consolidated 
financial statements for the fiscal year ending December 31, 1998.

In June 1997, the Financial Accounting Standards Board issued Statement of 
Financial Accounting Standards No. 131 "Disclosures about Segments of a 
Business Enterprise" (SFAS 131) which will be effective for financial 
statements beginning after December 15, 1997, and establishes standards for 
disclosures about segments of an enterprise.  Earlier application is 
encouraged.  The Company will make the required disclosures under SFAS 131 in 
its consolidated financial statements for the year ended December 31, 1998.


                                       11
<PAGE>

PART II.       OTHER INFORMATION


    Item 6:   Exhibits and Reports on Form 8-K

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

              (b)  Exhibit 27 - Financial Data Schedule

              (c)  There were no reports on Form 8-K during the quarter ended
                   September 30, 1997.



                                       12
<PAGE>

                           MOLECULAR DYNAMICS, INC.
                                       
                                       
                                  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.

                                        MOLECULAR DYNAMICS, INC.
                                             (Registrant)


Date:  November 11, 1997          By:    /s/  Jay Flatley
       -----------------              ------------------------------------------
                                              Jay Flatley
                                              President, Chief  Executive
                                              Officer & Chief Financial Officer


Date:  November 11, 1997          By:    /s/  Lynne R. Wagoner
       -----------------              ------------------------------------------
                                              Lynne R. Wagoner
                                              Director of Finance
                                                (Principal Accounting Officer)


                                       13
<PAGE>


                                 EXHIBIT INDEX


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

     (b)  Exhibit 27 - Financial Data Schedule