<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 JUNE 30, 1999

                                       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 000-23541

                                  NANOGEN, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

             DELAWARE                                  33-0489621
  (State or other jurisdiction of                   (I.R.S. Employer
  incorporation or organization)                  Identification No.)


       10398 PACIFIC CENTER COURT, SAN DIEGO, CA              92121
       (Address of principal executive offices)            (Zip code)


                                 (858) 410-4600
              (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
           -------             -------


AS OF JULY 21, 1999, 18,871,077 SHARES OF THE REGISTRANT'S COMMON STOCK WERE
OUTSTANDING.

<PAGE>

                                  NANOGEN, INC.
                                    FORM 10-Q
                                      INDEX

<TABLE>
<CAPTION>

                                                                                                   PAGE
                                                                                                   ----
<S>               <C>                                                                              <C>
PART I.           FINANCIAL INFORMATION

Item 1.           Financial Statements:

                  Consolidated Balance Sheets at June 30, 1999
                    and December 31, 1998...........................................................3

                  Consolidated Statements of Operations for the Three and
                    Six Months ended June 30, 1999 and 1998.........................................4

                  Consolidated Statements of Cash Flows for the Three and
                    Six Months ended June 30, 1999 and 1998.........................................5

                  Notes to Consolidated Financial Statements........................................6

Item 2.           Management's Discussion and Analysis of Financial
                  Condition and Results of Operations...............................................7

Item 3.           Quantitative and Qualitative Disclosures About Market Risk........................14


PART II:          OTHER INFORMATION

Item 2.           Changes in Securities and Use of Proceeds.........................................16

Item 4.           Submission of Matters to a Vote of Security Holders...............................16

Item 6.           Exhibits and Reports on Form 8-K..................................................17

SIGNATURES..........................................................................................18

EXHIBIT INDEX.......................................................................................19

</TABLE>

                                      -2-

<PAGE>

                          PART I. FINANCIAL INFORMATION
                          ITEM 1. FINANCIAL STATEMENTS
                                  NANOGEN, INC.
                           CONSOLIDATED BALANCE SHEETS
                        (IN THOUSANDS, EXCEPT SHARE DATA)

<TABLE>
<CAPTION>

                                                                              JUNE 30,           DECEMBER 31,
                                                                                1999                 1998
                                                                          -----------------     ----------------
                                                                           (unaudited)
                                 ASSETS
<S>                                                                      <C>                   <C>
Current assets:
  Cash and cash equivalents                                               $   48,304            $   62,245
  Receivables and other current assets                                         3,442                 2,933
                                                                          --------------        -------------
Total current assets                                                          51,746                65,178

Property and equipment, net                                                    6,911                 6,980
Restricted cash                                                                  277                   270
Other assets                                                                     226                   276
                                                                          --------------       --------------
                                                                          $   59,160            $   72,704
                                                                          ==============        =============

</TABLE>

                  LIABILITIES AND STOCKHOLDERS' EQUITY

<TABLE>
<CAPTION>

<S>                                                                      <C>                   <C>
Current liabilities:
  Accounts payable                                                        $    1,071            $    1,066
  Accrued liabilities                                                          1,828                 1,433
  Deferred revenue                                                             2,053                 3,065
  Current portion of capital lease obligations                                 2,088                 1,913
                                                                          --------------        -------------
Total current liabilities                                                      7,040                 7,477

Capital lease obligations, less current portion                                3,831                 4,176

Stockholders' equity:
  Convertible preferred stock, $.001 par value, 5,000,000 shares
    authorized; no shares issued and outstanding at June 30, 1999
    and December 31, 1998                                                          -                     -

  Common stock, $.001 par value, 50,000,000 shares authorized;
    18,870,382 and 18,835,461 shares issued and outstanding
    at June 30, 1999 and December 31, 1998, respectively                          19                    19
  Additional paid-in capital                                                 111,603               111,489
  Deferred compensation                                                         (951)               (1,512)
  Notes receivable from officers                                              (1,559)               (1,514)
  Accumulated deficit                                                        (60,823)              (47,431)
                                                                          --------------        -------------
Total stockholders' equity                                                    48,289                61,051
                                                                          --------------        -------------
                                                                          $   59,160            $   72,704
                                                                          ==============        =============

</TABLE>

                             See accompanying notes.

                                      -3-

<PAGE>

                                  NANOGEN, INC.
                      CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (UNAUDITED)
                      (IN THOUSANDS, EXCEPT PER SHARE DATA)

<TABLE>
<CAPTION>

                                                    THREE MONTHS ENDED JUNE 30,         SIX MONTHS ENDED JUNE 30,
                                                   -------------------------------    -------------------------------
                                                       1999             1998              1999             1998
                                                   --------------   --------------    --------------   --------------
<S>                                                  <C>               <C>               <C>              <C>
Revenues:
  Sponsored research                                  $  1,566          $  1,387          $  2,919         $  2,272
  Contract and grant revenue                               639               550             1,216            1,097
                                                   --------------   --------------    --------------   --------------
Total revenues                                           2,205             1,937             4,135            3,369

Operating expenses:
  Research and development                               6,776             5,066            13,636            9,712
  General and administrative                             2,160             1,482             3,997            2,952
  Acquired in-process technology                             -                 -                 -            1,193
                                                   --------------   --------------    --------------   --------------
Total operating expenses                                 8,936             6,548            17,633           13,857
                                                   --------------   --------------    --------------   --------------
Loss from operations                                    (6,731)           (4,611)          (13,498)         (10,488)

Interest income (expense), net                             503              805              1,071              964
Loss on disposition of fixed assets                        (30)               -                (30)               -
Equity in loss of joint venture                           (275)               -               (935)               -
                                                   --------------   --------------    --------------   --------------
Net loss                                              $ (6,533)        $ (3,806)         $ (13,392)        $ (9,524)
                                                   ==============   ==============    ==============   ==============

Net loss per share -
  basic and diluted                                   $  (0.36)        $  (0.25)         $  (0.75)        $  (1.11)
                                                   ==============   ==============    ==============   ==============

Number of shares used in computing
  net loss per share - basic and diluted                18,073           15,346            17,960            8,584
                                                   ==============   ==============    ==============   ==============

</TABLE>

                             See accompanying notes.

                                      -4-

<PAGE>

                                  NANOGEN, INC.
                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)
                                 (IN THOUSANDS)

<TABLE>
<CAPTION>

                                                                                SIX MONTHS ENDED JUNE 30,
                                                                          --------------------------------------
                                                                               1999                   1998
                                                                          --------------        ----------------
<S>                                                                       <C>                    <C>
Cash flows from operating activities:
Net loss                                                                   $ (13,392)             $ (9,524)
Adjustments to reconcile net loss to net cash
  used in operating activities:
  Acquisition of in-process technology                                             -                 1,193
  Depreciation and amortization                                                  833                   411
  Amortization of deferred compensation                                          561                 1,378
  Loss on dispositon of fixed assets, net                                         30                     -
  Equity in loss of joint venture                                                935                     -
  Changes in operating assets and liabilities:
    Accounts payable                                                               5                   706
    Accrued liabilities                                                          395                   216
    Deferred revenue                                                          (1,012)                  611
    Receivables and other current assets                                        (423)               (1,167)
                                                                          --------------        -------------
Net cash used in operating activities                                        (12,068)               (6,176)

Cash flows from investing activities:
Purchase of equipment                                                            (34)
Investment in joint venture                                                     (935)                    -
                                                                          --------------        -------------
Net cash used in investing activities                                           (969)                    -

Cash flows from financing activities:
Restricted cash                                                                   (7)                  (10)
Principal payments on capital lease obligations                                 (966)                 (617)
Issuance of common stock, net of repurchases                                     114                60,077
Interest on notes receivable from officers                                       (45)                  (31)
Other assets                                                                       -                   (58)
                                                                          --------------        -------------
Net cash provided by (used in) financing activities                             (904)               59,361

Increase/(decrease) in cash and cash equivalents                             (13,941)               53,185
Cash and cash equivalents at beginning of period                              62,245                19,498
                                                                          --------------        -------------
Cash and cash equivalents at end of period                                  $ 48,304              $ 72,683
                                                                          ==============        =============

Supplemental disclosure of cash flow information:
    Interest paid                                                         $      306            $      187
                                                                          ==============        =============

Supplemental schedule of noncash investing and financing activities:
    Equipment acquired under capital leases                                $     760             $   4,457
                                                                          ==============        =============
    Common stock issued in exchange for notes
      receivable from officers                                            $          -          $      310
                                                                          ==============        =============
    Issuance of convertible preferred stock and
      warrants in exchange for in-process technology                      $          -           $   1,193
                                                                          ==============        =============

</TABLE>

                             See accompanying notes.

                                      -5-

<PAGE>

                                  NANOGEN, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  JUNE 30, 1999


1.  BASIS OF PRESENTATION

    The accompanying unaudited consolidated financial statements have been
    prepared in accordance with generally accepted accounting principles for
    interim financial information and with the instructions to Form 10-Q and
    Article 10 of Regulation S-X. Accordingly, they do not include all of the
    information and footnotes required by generally accepted accounting
    principles for complete financial statements. The consolidated balance
    sheet as of June 30, 1999, consolidated statements of operations for the
    three and six months ended June 30, 1999 and 1998, and the consolidated
    statements of cash flows for the six months ended June 30, 1999 and 1998
    are unaudited, but include all adjustments (consisting of normal recurring
    adjustments) which the Company considers necessary for a fair presentation
    of the financial position, results of operations and cash flows for the
    periods presented. The results of operations for the three and six months
    ended June 30, 1999 shown herein are not necessarily indicative of the
    results that may be expected for the year ended December 31, 1999.

    For more complete financial information, these financial statements, and
    notes thereto, should be read in conjunction with the audited consolidated
    financial statements for the year ended December 31, 1998 included in the
    Nanogen, Inc. Form 10-K filed with the Securities and Exchange Commission.

    NET LOSS PER SHARE

    The Company computes net income per share in accordance with SFAS No. 128,
    "Earnings per Share" and SEC Staff Accounting Bulletin No. 98 ("SAB 98").
    Under the provisions of SFAS No. 128 and SAB 98, basic net income per share
    is computed by dividing the net income available to common stockholders for
    the period by the weighted average number of common shares outstanding
    during the period. Diluted net income per share is computed by dividing the
    net income for the period by the weighted average number of common shares
    outstanding during the period and dilutive potential common shares
    outstanding. Weighted average common shares outstanding during the period
    does not include shares issued pursuant to the exercise of stock options
    prior to vesting. Due to the losses incurred by the Company during the
    three and six months ended June 30, 1999 and 1998, common stock equivalents
    resulting from the assumed exercise of outstanding stock options and
    warrants have been excluded from the computation of diluted net loss per
    share as their effect would be anti-dilutive.

2.  BECTON, DICKINSON AND COMPANY PARTNERSHIP

    The Company is collaborating with Becton, Dickinson and Company ("Becton
    Dickinson") to develop and commercialize products in the field of IN VITRO
    nucleic acid-based diagnostic and monitoring technologies. Pursuant to a
    Master Agreement entered into between the two parties, Becton Dickinson and
    Nanogen agreed to form The Nanogen/Becton Dickinson Partnership (the
    "Partnership"). Pursuant to a General Partnership Agreement, Becton
    Dickinson and Nanogen have contributed to the Partnership their respective
    rights under a Collaborative Research and Development Agreement established
    in May 1997, certain Intellectual Property Licenses and, as of June 30,
    1999 cash in the amount in aggregate of approximately $8.3 million, of
    which approximately $6.8 million was paid by Becton Dickinson and
    approximately $1.5 million was paid by Nanogen. The amounts paid by Nanogen
    during the six months ended June 30, 1999 have been recorded as Nanogen's
    share of the joint venture's loss for that period. The General Partnership
    Agreement also contemplates additional research funding aggregating up to
    approximately $12.9 million, of which up to $4.0 million is to be paid by
    Nanogen, during the period from July 1, 1999 through April 1, 2001,
    conditioned upon the achievement of milestones to be mutually agreed upon
    by the partners. There can be no assurances that the parties will agree to
    such milestones, and if agreed upon, there can be no assurances that these
    milestones will be achieved in a timely fashion, if at all. In July 1999,
    Nanogen and Becton Dickinson announced that scheduled program objectives
    for the first half of 1999 had been achieved. In addition to the
    above-described payments, Becton Dickinson and Nanogen have agreed to
    contribute additional amounts to fund marketing and manufacturing startup.

                                      -6-

<PAGE>

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

    This report includes forward-looking statements about our business and
results of operations that are subject to risks and uncertainties that could
cause our actual results to vary materially from those reflected in the
forward-looking statements. Words such as "believes," "anticipates," "plans,"
"estimates," "future," "could," "may," "should," "expect," "envision,"
"potentially," variations of such words and similar expressions are intended
to identify such forward-looking statements. Factors that could cause or
contribute to these differences include those discussed below under the
caption "Factors that May Affect Results" and elsewhere in this Form 10-Q.
Readers are cautioned not to place undue reliance on these forward-looking
statements which speak only as of the date hereof. We disclaim any intent or
obligation to update these forward-looking statements.

OVERVIEW

    Since commencing operations in 1993, we have applied substantially all of
our resources to our research and development programs. We have incurred
losses since inception and, as of June 30, 1999, had an accumulated deficit
of approximately $60.8 million. We expect to incur significant losses over at
least the next several years as we expand our research and product
development efforts and attempt to commercialize our products.

    We currently have no products available for sale and no revenues have
been generated from the sale of products arising out of our technology. We
anticipate our main sources of revenues during at least 1999 will be payments
from contracts, grants and sponsored research. We believe our future
operating results may be subject to quarterly fluctuations due to a variety
of factors, including the achievement of milestones under our collaborative
agreements, whether and when new products are successfully developed and
introduced by us or our competitors, and market acceptance of products under
development. Payments under contracts, grants and sponsored research
agreements will be subject to significant fluctuations in both timing and
amount and therefore our results of operations for any period may not be
comparable to the results of operations for any other period.

RESULTS OF OPERATIONS

    REVENUES. For the three and six months ended June 30, 1999, revenue from
sponsored research totaled approximately $1.6 million and $2.9 million,
compared to approximately $1.4 million and $2.3 million for the three and six
months ended June 30, 1998, respectively. Revenues are recorded under these
arrangements as expenses are incurred. Payments received in advance under
these arrangements are recorded as deferred revenue until the expenses are
incurred. Sponsored research revenue recognized during the three and six
months ended June 30, 1999 and 1998, was earned in connection with our joint
venture collaboration with Becton Dickinson, our research and development
agreement with Aventis Research and Technology ("Aventis", an affiliate of
Hoechst AG), and our nonexclusive research and development agreement with
Elan Corporation, plc ("Elan"). As of June 30, 1999, Nanogen and Elan have
not yet agreed upon specific program objectives with respect to the
nonexclusive research and development agreement.

    Revenue from contracts and grants totaled approximately $639,000 and $1.2
million for the three and six months ended June 30, 1999, compared to
approximately $550,000 and $1.1 million for the three and six months ended
June 30, 1998. The Company funds some of its research and development efforts
through contracts and grants awarded by various federal and state agencies.
Revenue was recognized under six such contracts and grants for the three and
six months ended June 30, 1999 as compared to seven such contracts and grants
for the same period in 1998. Revenues are recognized under these contracts
and grants as expenses are incurred.

    Continuation of sponsored research agreements, contracts and grants is
dependent upon us achieving specific contractual milestones. The recognition
of revenue under sponsored research agreements, contracts and grants may vary
from quarter to quarter and may result in significant fluctuations in
operating results from year to year.

    RESEARCH AND DEVELOPMENT EXPENSES. Research and development expenses
increased to approximately $6.8 and $13.6 million for the three and six
months ended June 30, 1999, from approximately $5.1 and $9.7 million for

                                      -7-
<PAGE>

the three and six months ended June 30, 1998. Research and development
expenses include salaries, lab supplies, consulting, travel, facilities,
product design and prototype development, and other expenditures relating to
research and product development. The increase in research and development
expenditures for the three and six months ended June 30, 1999, compared to
the same period in 1998, can be primarily attributed to costs associated with
the development and refinement of engineering prototypes as we move toward
commercialization of our first product. Additionally, the increases from year
to year are attributable to the continued growth of research and product
development efforts, including hiring of additional scientific, engineering
and operations personnel, increased purchases of laboratory supplies,
equipment and services to support the sponsored research programs with Becton
Dickinson, Aventis and Elan, and expansion of research and development
facilities. We expect research and development spending to increase over the
next several years as our research and product development efforts continue
to expand.

    GENERAL AND ADMINISTRATIVE EXPENSES. General and administrative expenses
totaled approximately $2.2 and $4.0 million for the three and six months
ended June 30, 1999, compared to approximately $1.5 and $3.0 million for the
three and six months ended June 30, 1998. This increase was principally due
to increased legal costs associated with enhancing and maintaining the
Company's intellectual property portfolio, the expansion of activities
related to marketing the Company's potential products, and to increased costs
associated with operating as a public company. The increase was partially
offset by a decrease in deferred compensation expense recognized in the first
six months of 1999 compared to what was recorded during the same period in
1998. Deferred compensation represents the excess of the fair value for
financial statement presentation purposes over the exercise price for common
stock issuable on exercise of stock options. General and administrative
expenses are expected to continue to increase as we continue to expand our
sales and marketing and general and administrative organizations and as we
continue to enhance our intellectual property portfolio.

    ACQUIRED IN-PROCESS TECHNOLOGY. During the first quarter of 1998, the
Company issued 200,000 shares of its Series D Convertible Preferred Stock at
$6.00 per share in exchange for all of the outstanding shares of Nanotronics,
Inc.. This Series D Preferred Stock converted into 132,334 shares of common
stock at the Company's initial public offering. The in-process technology
which was acquired relates generally to nanotechnology and molecular
electronics. Nanotronics' research is currently partially funded through
government contracts from the Information Directorate of the United States
Air Force Research Laboratory. We recorded $1.2 million in expenses relating
to acquired in-process technology during the three months ended March 31,
1998.

    INTEREST INCOME (EXPENSE), NET. During the three months ended June 30,
1999, the Company had net interest income of approximately $503,000, compared
to net interest income of approximately $805,000 for the same period during
1998. The decrease in net interest income for the three months ended June 30,
1999 compared to the same period in 1998 can be attributed to the lower cash
balances available during this period in 1999 compared to 1998 as a result of
cash used for operations. In addition, interest rates were lower in 1999 as
compared to 1998. For the six months ended June 30, 1999, the Company had net
interest income of approximately $1.1 million, compared to net interest
income of approximately $964,000 for the same period in 1998. The increase in
net interest income can be attributed to larger average cash balances during
the first six months of 1999, compared to the same period in 1998. Interest
expense during the six months ended June 30, 1999 was greater than interest
expense during the same period in 1998, due to a greater amount of equipment
under capital leases in 1999.

    EQUITY IN LOSS OF JOINT VENTURE. The Company recognized a loss of
approximately $275,000 and $935,000 for the three and six months ended June
30, 1999 from the joint venture with Becton Dickinson, based on the loss
allocation described in the Partnership Agreement stating that losses will be
allocated in proportion to and not to exceed required cash contributions.
There was no loss recorded for the three and six months ended June 30, 1998,
as no cash contributions were required to be made by us to the joint venture
during that period.

LIQUIDITY AND CAPITAL RESOURCES

    We have financed our operations to date primarily through private
placements of equity securities totaling approximately $65.1 million, as well
as through our initial public offering in April 1998 which generated net
proceeds of approximately $38.7 million.
                                      -8-
<PAGE>

    To date we have funded most of our equipment acquisitions and leasehold
improvements through capital leasing or secured debt facilities. During the
first six months of 1999, we received proceeds from equipment financing of
approximately $760,000. This compares to $4.5 million received for equipment
acquisitions and leasehold improvements during the same period in 1998 which
was primarily related to the expansion of our research and administrative
facility. We anticipate that we will continue to use capital equipment
leasing or debt facilities to fund most of our equipment acquisitions and
leasehold improvements.

    Net cash used in operating activities was approximately $12.1 million and
$6.2 million for the six months ended June 30, 1999 and 1998, respectively.
Cash used for operations was primarily related to costs associated with
developing prototypes of our initial product, the support of our expanding
operations, including higher personnel costs, and legal fees relating to
establishing and maintaining our intellectual property rights.

    At June 30, 1999, we had approximately $48.3 million in cash and cash
equivalents. We expect that our existing capital resources, combined with
anticipated revenues from potential product sales, sponsored research
agreements, contracts and grants will be sufficient to support our planned
operations into the year 2001. This estimate of the period for which we
expect our available sources of liquidity to be sufficient to meet our
capital requirements is a forward-looking statement that involves risks and
uncertainties, and actual results may differ materially. Our future liquidity
and capital funding requirements will depend on numerous factors including,
but not limited to, the extent to which our products under development are
successfully developed and gain market acceptance, the timing of regulatory
actions regarding our potential products, the costs and timing of expansion
of sales, marketing and manufacturing activities, prosecution and enforcement
of patents important to our business, the results of clinical trials,
competitive developments, and our ability to maintain existing collaborations
and to enter into additional collaborative arrangements. We have incurred
negative cash flow from operations since inception and do not expect to
generate positive cash flow to fund our operations for at least the next
several years. We may need to raise additional capital to fund our research
and development programs, to scale up manufacturing activities and expand our
sales and marketing efforts to support the commercialization of our products
under development. Additional capital may not be available on terms
acceptable to us, or at all. If adequate funds are not available, we may be
required to curtail our operations significantly or to obtain funds through
entering into collaborative agreements or other arrangements on unfavorable
terms. Our failure to raise capital on acceptable terms when needed could
have a material adverse effect on our business, financial condition or
results of operations.

YEAR 2000 ISSUES

    The Year 2000 issue arises from the fact that many existing computer
software programs use only the last two digits to refer to a specific year,
instead of all four digits. As a result, computer programs that have
date-sensitive software, or operate with date-sensitive data, may recognize a
date using "00" as the year 1900 rather than the year 2000. This could result
in a system failure or miscalculation causing disruptions in operations,
including, among other things, the temporary inability to process
transactions or engage in normal business activities.

    We have assembled a Year 2000 task force to ensure that we are Year 2000
compliant by December 31, 1999. Our task force, assisted by third parties, is
currently assessing and testing our computer systems, software applications,
equipment and facilities infrastructure to ensure that all systems will
function properly with respect to dates in the Year 2000 and thereafter. To
date, we have not become aware of any significant modifications or
conversions of existing software or hardware which will be required. We
expect to complete our assessment and testing during August 1999. Any
required modifications and conversions of existing software and hardware are
expected to be completed by September 30, 1999.

    We have initiated formal communications with our significant suppliers of
products and services and key business partners in order to determine their
level of Year 2000 compliance. We will continue to seek information from
non-responsive suppliers. In the event that any of our significant suppliers
do not successfully achieve Year 2000 compliance in a timely manner, our
results of operations could be adversely affected. There can be no assurance
that the systems of other companies on which our systems rely will be
converted on a timely basis and would not have an adverse effect on our
results of operations.
                                      -9-
<PAGE>

    Although no significant issues have arisen during our assessment
procedures, we are currently developing specific contingency plans intended
to mitigate the effects of any potential Year 2000 disruption. We have
determined that a reasonable "worst case" scenario relates to Year 2000
compliance problems of our suppliers of products and services and other
external organizations which if not remedied could adversely affect our
results of operations.

    The cost we expect to incur to achieve Year 2000 compliance for our
internal systems and equipment should be less than $150,000. Costs incurred
to date have not been material.

FACTORS THAT MAY AFFECT RESULTS

OUR PRODUCTS MAY NOT BE SUCCESSFULLY DEVELOPED, WHICH WOULD ADVERSELY AFFECT
US

    All of our products are under development. Our products may not be
successfully developed or commercialized on a timely basis, or at all. If we
are unable, for technological or other reasons, to complete the development,
introduction or scale-up of manufacturing of our new products, or if our
products do not achieve a significant level of market acceptance, we would be
adversely affected.

    Our success will depend upon our ability to overcome significant
technological challenges and successfully introduce products into the
marketplace. A number of applications envisioned by us will require
significant enhancements in our basic technology platform.

LACK OF MARKET ACCEPTANCE OF OUR TECHNOLOGY WOULD ADVERSELY AFFECT US

    We may not be able to develop commercially viable products. Even if a
product is developed it may not be accepted in the marketplace. If we are
unable to achieve market acceptance, we would be adversely affected. Market
acceptance will depend on many factors, including demonstrating to customers
that our technology platform is a viable alternative to currently available
technologies. In addition, our technology platform could be adversely
affected by limited funding available for capital acquisitions by our
customers, as well as internal obstacles to customer approvals of purchases
of our products.

OUR DEPENDENCE ON COLLABORATIVE ALLIANCES COULD ADVERSELY AFFECT US

    The development and commercialization of our products in a number of
applications depends on the formation of alliances and licensing
arrangements. We may not be successful in entering into or maintaining
collaborations to develop these commercial applications. Failure to do so
could have an adverse impact on us. We may have limited or no control over
the time, effort or financial resources that any partner may devote to the
development or marketing of our products.

    We may be materially and adversely affected if:

         -    A partner develops competitive technologies;

         -    We are precluded from entering into competitive arrangements
              with other potential partners;

         -    Disputes arise over ownership rights to any intellectual
              property, know-how or technologies developed with a partner; or

         -    An agreement is terminated early, or by a failure by a partner to
              devote sufficient resources to the development and
              commercialization of our products.

    We currently have agreements with Becton Dickinson, Aventis and Elan that
contemplate the commercialization of products resulting from research and
development collaboration agreements between the parties. These
collaborations may not be successful.

                                      -10-

<PAGE>

OUR HISTORY OF LOSSES AND OUR ANTICIPATION OF FUTURE LOSSES MAY ADVERSELY
AFFECT US

    At June 30, 1999, we had an accumulated deficit of approximately $60.8
million. We anticipate that we will continue to incur operating losses for at
least the next several years. We may never attain profitability or become
profitable on a quarterly or annual basis in the future. We currently have no
products available for sale and to date no revenues have been generated from
commercialization of products arising out of our technology.

    To develop and sell our products successfully, we will need to increase
our spending levels in research and development, as well as in selling,
marketing, and administration. We will have to incur these increased spending
levels before knowing whether our products can be sold successfully.

    Our anticipated increases in operating expenses may adversely affect our
financial prospects.

FAILURE TO RAISE ADDITIONAL CAPITAL MAY ADVERSELY AFFECT US

    We have incurred negative cash flow from operations since inception. We
do not expect to generate positive cash flow to fund our operations for at
least the next several years. We may need to raise additional capital to fund
our research and development programs, to scale up manufacturing activities
and establish our sales and marketing capability. Our current collaborations
will, and future collaborations may, require us to commit substantial amounts
of capital. We may not be able to make these capital contributions.

    If adequate funds are not available, we may be required to curtail our
operations significantly or to obtain funds by entering into collaborative
agreements or other arrangements on less favorable terms. Our failure to
raise capital on acceptable terms when needed could have a material adverse
effect on us. Our liquidity and capital funding requirements will depend on
numerous factors, including:

         -    The extent to which our products under development are
              successfully developed and gain market acceptance;

         -    The timing of regulatory actions regarding our potential
              products;

         -    The costs and timing of expansion of sales, marketing and
              manufacturing activities;

         -    Prosecution and enforcement of patents important to our business;

         -    The results of clinical trials, competitive developments, and our
              ability to enter into additional collaborative arrangements.

    Additional capital may not be available on terms acceptable to us, or at
all. Any additional equity financing may be dilutive to stockholders, and
debt financing, if available, may include restrictive covenants.

COMPETING TECHNOLOGIES MAY ADVERSELY AFFECT US

    We expect to encounter intense competition from a number of companies
that offer products in our targeted application areas. We anticipate that our
competitors in these areas will include:

         -    Health care companies that manufacture laboratory-based tests and
              analyzers,

         -    Diagnostic and pharmaceutical companies, and

         -    Companies developing drug discovery technologies.

    To the extent we are successful in developing products in these areas, we
will face competition from established companies and numerous development-stage
companies that continually enter these markets.


                                      -11-

<PAGE>

    In many instances, our competitors have substantially greater financial,
technical, research and other resources and larger, more established
marketing, sales, distribution and service organizations than us. Moreover,
these competitors may offer broader product lines and have greater name
recognition than us, and may offer discounts as a competitive tactic.

    In addition, several development stage companies are currently making or
developing products that compete with or will compete with our potential
products. Our competitors may succeed in developing or marketing technologies
or products that are more effective or commercially attractive than our
potential products, or that render our technologies and potential products
obsolete.

    Also, we may not have the financial resources, technical expertise or
marketing, distribution or support capabilities to compete successfully in
the future.

THE UNCERTAINTY OF PATENT AND PROPRIETARY TECHNOLOGY PROTECTION AND OUR
POTENTIAL INABILITY TO LICENSE TECHNOLOGY FROM THIRD PARTIES MAY ADVERSELY
AFFECT US

    Our success will depend in part on obtaining and maintaining meaningful
patent protection on our inventions, technologies and discoveries. Our
ability to compete effectively will depend on our ability to develop and
maintain proprietary aspects of our technology, and to operate without
infringing the proprietary rights of others, or to obtain rights to
third-party proprietary rights, if necessary. Our pending patent applications
may not result in the issuance of patents. Our patent applications may not
have priority over others' applications, and even if issued, any of our
patents may not offer protection against competitors with similar
technologies. Any patents issued to us may be challenged, invalidated or
circumvented and the rights created thereunder may not afford us a
competitive advantage.

    Our commercial success also depends in part on us neither infringing
valid, enforceable patents or proprietary rights of third parties, nor
breaching any licenses that may relate to our technologies and products. We
are aware of third-party patents that may relate to our technology. It is
possible that we may unintentionally infringe these patents or other patents
or proprietary rights of third parties. We have received and may in the
future receive notices claiming infringement from third parties as well as
invitations to take licenses under third-party patents. Any legal action
against us or our collaborative partners claiming damages and seeking to
enjoin commercial activities relating to our products and processes affected
by third-party rights, may require us or our collaborative partners to obtain
licenses in order to continue to manufacture or market the affected products
and processes. In addition, these actions may subject us to potential
liability for damages. We or our collaborative partners may not prevail in an
action and any license required under a patent may not be made available on
commercially acceptable terms, or at all.

    There are a significant number of U.S. and foreign patents and patent
applications held by third parties in our areas of interest, and we believe
that there may be significant litigation in the industry regarding patent and
other intellectual property rights. If we become involved in litigation, it
could consume a substantial portion of our managerial and financial
resources, which could have a material adverse effect on us. Additionally,
the defense and prosecution of interference proceedings before the U.S.
Patent and Trademark Office ("USPTO") and related administrative proceedings
would result in substantial expense to us and significant diversion of effort
by our technical and management personnel. We may in the future become
subject to USPTO interference proceedings to determine the priority of
inventions. In addition, laws of some foreign countries do not protect
intellectual property to the same extent as do laws in the U.S., which may
subject us to additional difficulties in protecting our intellectual property
in those countries.

    We also rely upon trade secrets, technical know-how and continuing
inventions to develop and maintain our competitive position. Others may
independently develop substantially equivalent proprietary information and
techniques or otherwise gain access to our trade secrets or disclose our
technology and we may not be able to meaningfully protect our trade secrets,
or be capable of protecting our rights to our trade secrets. We seek to
protect our technology and patents, in part, by confidentiality agreements
with our employees and contractors. Our employees may breach their existing
Proprietary Information, Inventions, and Dispute Resolution Agreements and
these agreements may not protect our intellectual property. This could have a
material adverse effect on us.
                                      -12-
<PAGE>

FAILURE TO OBTAIN REGULATORY APPROVALS WOULD ADVERSELY AFFECT US

    We anticipate that the manufacturing, labeling, distribution and
marketing of a number of our diagnostic products will be subject to
regulation in the U.S. and other countries. We may not be able to obtain
necessary regulatory approvals or clearances for our products on a timely
basis, or at all. Delays in receipt of or failure to receive approvals or
clearances, the loss of previously received approvals or clearances,
limitations on intended uses imposed as a condition of approvals or
clearances, or failure to comply with existing or future regulatory
requirements would have a material adverse effect on us.

    In the U.S., the Food and Drug Administration ("FDA") regulates, as
medical devices, most diagnostic tests and IN VITRO reagents that are
marketed as finished test kits and equipment. Pursuant to the Federal Food,
Drug, and Cosmetic Act, the FDA regulates the preclinical and clinical
testing, design, efficacy, safety, manufacture, labeling, distribution and
promotion of medical devices. We will not be able to commence marketing or
commercial sales in the U.S. of these products until we receive clearance or
approval from the FDA, which can be a lengthy, expensive and uncertain
process. We have not applied for FDA or other regulatory approvals with
respect to any of our products under development. We may experience
difficulties that could delay or prevent the successful development,
introduction and marketing of new products. Regulatory clearance or approval
or clearance of any new products may not be granted by the FDA or foreign
regulatory authorities on a timely basis, if at all.

    Noncompliance with applicable FDA requirements can result in:

         -    Administrative sanctions or judicially imposed sanctions such as
              injunctions,

         -    Civil penalties, recall or seizure of products,

         -    Total or partial suspension of production, failure of the
              government to grant premarket clearance or premarket approval for
              devices,

         -    Withdrawal of marketing clearances or approvals, and

         -    Criminal prosecution.

    The FDA also has the authority to request recall, repair, replacement or
refund of the cost of any device manufactured or distributed by us. Any devices
manufactured or distributed by us pursuant to FDA clearance or approvals are
subject to pervasive and continuing regulation by the FDA and certain state
agencies.

OUR DEPENDENCE ON SUPPLIERS MAY ADVERSELY AFFECT US

    Key components and raw materials used in the manufacture of our products
are provided from limited sources or in some cases by single-source vendors.
Although we believe that alternative sources for these components and raw
materials are available, any supply interruption in a sole-sourced component
of raw material would have a material adverse effect on our ability to
manufacture our products until a new source of supply is qualified and, as a
result, could have a material adverse effect on us. In addition, an
uncorrected impurity or supplier's variation in a raw material, either
unknown to us or incompatible with our manufacturing process, could have a
material adverse effect on our ability to manufacture products. We may be
unable to find a sufficient alternative supply channel in a reasonable time
period, or on commercially reasonable terms, if at all. Failure to obtain a
supplier for the manufacture of components of our future products, if any,
could have a material adverse effect on us.

OUR LIMITED MANUFACTURING EXPERIENCE AND POTENTIAL INABILITY TO SCALE UP
MANUFACTURING COULD ADVERSELY AFFECT US

    We have no experience manufacturing products for commercial purposes. We
rely on subcontractors to manufacture the limited quantities of semiconductor
microchips and other components we require for internal and collaborative
purposes, as well as for use in clinical trials and prototype products.

                                      -13-

<PAGE>

    Manufacturing, supply and quality control problems may arise as we either
alone or with subcontractors attempt to scale up manufacturing procedures.
Scale-up may not be achieved in a timely manner or at a commercially
reasonable cost. Any failure to surmount problems could lead to delays or
pose a threat to the ultimate commercialization of our products and result in
a material adverse effect on us.

    If we or any of our contract manufacturers encounter manufacturing
difficulties, including:

         -    The ability to scale up manufacturing capacity,
         -    Production yields,
         -    Quality control and assurance, or
         -    Shortages of components or qualified personnel,
              it could have a material adverse effect on us.

    Our manufacturing facilities and those of our contract manufacturers are
or will be subject to periodic regulatory inspections by the FDA and other
federal and state regulatory agencies and these facilities are subject to
Quality System Regulation ("QSR") requirements of the FDA. Failure by us or
our third-party manufacturers to maintain its facilities in accordance with
QSR regulations, other international quality standards or other regulatory
requirements would have a material adverse effect on us.

OUR LIMITED MARKETING AND SALES CAPABILITY COULD ADVERSELY AFFECT US

    We have limited product marketing and sales capabilities. In attracting,
establishing and maintaining a marketing and sales force, or entering into
third-party marketing or distribution arrangements with other companies, we
expect to incur significant additional expenses. We may not be able to
successfully establish a sales and marketing capability or enter into
third-party marketing or distribution arrangements or be successful in
achieving marketplace acceptance for our products. This failure would have a
material adverse affect on us.

A FAILURE TO MANAGE OUR GROWTH MAY ADVERSELY AFFECT US

    We expect to continue to experience growth in the number of our employees
and the scope of our operating and financial systems. This growth has
resulted in an increase in responsibilities for both existing and new
management personnel. Our ability to manage growth effectively will require
us to continue to implement and improve our operational, financial and
management information systems and to recruit, train, motivate and manage our
employees. We may not be able to manage our growth and expansion, and a
failure to do so could have a material adverse effect on us.

OUR PRODUCT LIABILITY EXPOSURE AND THE INADEQUACY OR UNAVAILABILITY OF
INSURANCE COVERAGE COULD ADVERSELY AFFECT US

    The testing, manufacturing and marketing of our products entails an
inherent risk of product liability claims. Any claims against us could have a
material adverse effect on us. We may not be able to obtain insurance on
acceptable terms with adequate coverage, or at reasonable costs. Potential
product liability claims may exceed the amount of our insurance coverage or
may be excluded from coverage under the terms of the policy. Our insurance
once obtained may not be renewed at a cost and level of coverage comparable
to that then in effect.

ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The Company invests its excess cash primarily in U.S. government securities
and marketable debt securities of financial institutions and corporations
with strong credit ratings. These instruments have maturities of ninety days
or less when acquired. We do not utilize derivative financial instruments,
derivative commodity instruments or other market risk sensitive instruments,
positions or transactions in any material fashion. Accordingly, we believe

                                      -14-

<PAGE>

that, while the instruments we hold are subject to changes in the financial
standing of the issuer of such securities, we are not subject to any material
risks arising from changes in interest rates, foreign currency exchange
rates, commodity prices, equity prices or other market changes that affect
market risk sensitive instruments.

                                      -15-

<PAGE>

                                  NANOGEN, INC.
                           PART II - OTHER INFORMATION


ITEM 2.  CHANGES IN SECURITIES AND USE OF PROCEEDS

      (a)   Not applicable.

      (b)   Not applicable.

      (c)   Not applicable.

      (d)   On April 13, 1998, our Registration Statement on Form S-1 (File No.
            333-42791) was declared effective by the Securities and Exchange
            Commission (the "IPO Registration Statement"). The IPO Registration
            Statement registered a total of 3,900,000 shares of common stock,
            all of which were issued and sold by us (the "Offering") upon the
            termination of the Offering in April 1998. The Offering was led by
            a group consisting of Morgan Stanley Dean Witter, Lehman Brothers
            and SBC Warburg Dillion Read Inc. The shares sold by us were sold
            at an aggregate offering price of $42.9 million, netting proceeds
            of approximately $38.7 million to us after underwriting fees of
            approximately $3.0 million and other offering expenses of
            approximately $1.2 million. None of these fees and expenses were
            paid to any director, officer, or 10% or greater stockholder of the
            Company or an affiliate of these persons.

            Since the effective date of the IPO Registration Statement, the net
            offering proceeds have been applied to the following uses in the
            following approximate amounts:

                  Repayment of indebtedness       $     2,830,000
                  Working capital                 $    26,213,000
                  Temporary investments           $     9,657,000

            The temporary investments specified above consist primarily of
            highly liquid investments which include marketable debt securities
            of financial institutions and corporations with strong credit
            ratings with maturities of ninety days or less when acquired. None
            of the payments noted above have been paid to any director,
            officer, or 10% or greater stockholder of the Company or an
            affiliate of these persons.

ITEM 4.  SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

      (a)   On June 30, 1999, the Registrant held its Annual Meeting of
Stockholders.

      (b)   As listed below, all of management's nominees for directors were
elected at the meeting:

<TABLE>
<CAPTION>
               Name of Nominee            No. of Votes For        No. of Votes Withheld      No. of Votes Abstain
               ---------------            ----------------        ---------------------      --------------------
         <S>                              <C>                     <C>                        <C>
          Howard C. Birndorf               16,976,683                      4,750                         0
          Cam L. Garner                    16,976,538                      4,895                         0
</TABLE>

            In addition, directors whose term of office continue after the
            Annual Meeting are: Tina S. Nova, Brook H. Byers, David G.
            Ludvigson, and Thomas G. Lynch.

      (c)   (1) The proposal to amend the Company's 1997 Stock Incentive Plan
                to increase the number of shares reserved for issuance
                thereunder by 925,000 was approved with 15,540,810 shares
                voting in favor, 1,406,260 voting against, 34,363 shares
                abstaining.

            (2) The appointment of Ernst & Young LLP as independent auditors of
                the Company for the fiscal year ending December 31, 1999 was
                ratified with 16,952,669 shares voting in favor, 3,360 voting
                against, 25,404 shares abstaining.

                                      -16-
<PAGE>

ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K

      (d)   Exhibits

            27.1     Financial Data Schedule.

      (b)   Reports on Form 8-K

              No Reports on Form 8-K were filed during the six months ended
              June 30, 1999.


                                      -17-

<PAGE>

                                  NANOGEN, 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.

                                                     NANOGEN, INC.



DATE           JULY 30, 1999                /S/ HOWARD C. BIRNDORF
          ------------------------         ----------------------------------
                                           HOWARD C. BIRNDORF
                                           CHAIRMAN OF THE BOARD AND CHIEF
                                           EXECUTIVE OFFICER
                                          (PRINCIPAL EXECUTIVE OFFICER)


DATE           JULY 30, 1999                /S/ DANIEL D. BURGESS
          ------------------------         ----------------------------------
                                           DANIEL D. BURGESS
                                           VICE PRESIDENT, CHIEF FINANCIAL
                                           OFFICER
                                           (PRINCIPAL FINANCIAL OFFICER)


                                      -18-

<PAGE>

                                  NANOGEN, INC.
                                  EXHIBIT INDEX

<TABLE>
<CAPTION>

   EXHIBIT NO.                          DESCRIPTION                      PAGE

<S>                                                                      <C>
27.1                Financial Data Schedule...............................20

</TABLE>

                                      -19-