<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 MARCH 31, 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)

                                   (619) 546-7700
              (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 MAY 10, 1999, 18,836,341 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 March 31, 1999
              and December 31, 1998...........................................3

            Consolidated Statements of Operations for the Three
              Months ended March 31, 1999 and 1998............................4

            Consolidated Statements of Cash Flows for the Three
              Months ended March 31, 1999 and 1998............................5

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

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

Item 3.     Quantitative and Qualitative Disclosures About Market Risk........15


PART II:    OTHER INFORMATION

Item 2.     Changes in Securities and Use of Proceeds.........................17

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>
                                                                             MARCH 31,           DECEMBER 31,
                                                                                1999                 1998
                                                                          -----------------     -------------
                                                                           (unaudited)
<S>                                                                      <C>                    <C>
                                 ASSETS

Current assets:
  Cash and cash equivalents                                               $   55,817            $   62,245
  Receivables and other current assets                                         3,088                 2,933
                                                                          --------------        -------------
Total current assets                                                          58,905                65,178

Property and equipment, net                                                    6,986                 6,980
Restricted cash                                                                  273                   270
Other assets                                                                     226                   276
                                                                          --------------        -------------
                                                                          $   66,390            $   72,704
                                                                          --------------        -------------
                                                                          --------------        -------------

                  LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
  Accounts payable                                                        $    1,436            $    1,066
  Accrued liabilities                                                          1,444                 1,433
  Deferred revenue                                                             2,306                 3,065
  Due to joint venture                                                           660                     -
  Current portion of capital lease obligations                                 2,092                 1,913
                                                                          --------------        -------------
Total current liabilities                                                      7,938                 7,477

Capital lease obligations, less current portion                                3,954                 4,176

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

  Common stock, $.001 par value, 50,000,000 shares authorized; 
   18,833,539 and 18,835,461 shares issued and outstanding
   at March 31, 1999 and December 31, 1998, respectively                          19                    19
  Additional paid-in capital                                                 111,503               111,489
  Deferred compensation                                                       (1,208)               (1,512)
  Notes receivable from officers                                              (1,526)               (1,514)
  Accumulated deficit                                                        (54,290)              (47,431)
                                                                          --------------        -------------
Total stockholders' equity                                                    54,498                61,051
                                                                          --------------        -------------
                                                                          $   66,390            $   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 MARCH 31,
                                                           ----------------------------------
                                                                 1999              1998
                                                           --------------     --------------
<S>                                                        <C>                <C>
Revenues:
  Sponsored research                                          $  1,353           $    885
  Contract and grant revenue                                       577                547
                                                           --------------     --------------
Total revenues                                                   1,930              1,432

Operating expenses:
  Research and development                                       6,860              4,646
  General and administrative                                     1,837              1,470
  Acquired in-process technology                                     -              1,193
                                                           --------------     --------------
Total operating expenses                                         8,697              7,309
                                                           --------------     --------------
Loss from operations                                            (6,767)            (5,877)

Interest income (expense), net                                     568                159
Equity in income (loss) of joint venture                          (660)                 -
                                                           --------------     --------------
Net loss                                                      $ (6,859)          $ (5,718)
                                                           --------------     --------------
                                                           --------------     --------------

Net loss per share -
  basic and diluted                                           $  (0.38)          $  (3.25)
                                                           --------------     --------------
                                                           --------------     --------------

Number of shares used in computing
  net loss per share - basic and diluted                        17,846              1,762
                                                           --------------     --------------
                                                           --------------     --------------
</TABLE>

                             See accompanying notes.

                                                                              4
<PAGE>

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

<TABLE>
<CAPTION>
                                                                              THREE MONTHS ENDED MARCH 31,
                                                                          -----------------------------------
                                                                              1999                  1998
                                                                          --------------        -------------
<S>                                                                       <C>                   <C>
Cash flows from operating activities:
Net loss                                                                    $ (6,859)             $ (5,718)
Adjustments to reconcile net loss to net cash
  used in operating activities:
  Acquisition of in-process technology                                             -                 1,193
  Depreciation and amortization                                                  419                   174
  Amortization of deferred compensation                                          304                   823
  Equity in loss of joint venture                                                660                     -
  Changes in operating assets and liabilities:
    Accounts payable                                                             370                  (162)
    Accrued liabilities                                                           11                  (136)
    Deferred revenue                                                            (759)                  793
    Receivables and other current assets                                         (69)                 (173)
                                                                          --------------        -------------
Net cash used in operating activities                                         (5,923)               (3,206)

Cash flows from investing activities:
Purchase of equipment                                                            (30)                    -
                                                                          --------------        -------------
Net cash used in investing activities                                            (30)                    -

Cash flows from financing activities:
Restricted cash                                                                   (3)                   (5)
Principal payments on capital lease obligations                                 (474)                 (297)
Issuance of common stock                                                          14                    75
Interest on notes receivable from officers                                       (12)                   (1)
Other assets                                                                       -                  (484)
                                                                          --------------        -------------
Net cash used in financing activities                                           (475)                 (712)

Decrease in cash and cash equivalents                                         (6,428)               (3,918)
Cash and cash equivalents at beginning of period                              62,245                19,498
                                                                          --------------        -------------
Cash and cash equivalents at end of period                                  $ 55,817              $ 15,580
                                                                          --------------        -------------
                                                                          --------------        -------------

Supplemental disclosure of cash flow information:
    Interest paid                                                          $     150            $       76
                                                                          --------------        -------------
                                                                          --------------        -------------

Supplemental schedule of noncash investing and financing activities:
    Equipment acquired under capital leases                                $     395             $   1,643
                                                                          --------------        -------------
                                                                          --------------        -------------
    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
                                 MARCH 31, 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 March 31, 1999, consolidated statements of operations for the three
    months ended March 31, 1999 and 1998, and the consolidated statements of
    cash flows for the three months ended March 31, 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 months ended March 31,
    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. Due to the losses incurred by the Company during the three
    months ended March 31, 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. In addition, based on interpretations by the
    Securities and Exchange Commission with respect to the treatment of
    preferred stock in computing certain earnings-per-share data, the Company
    has excluded preferred stock and preferred stock equivalents from the common
    stock equivalents calculation for the three months ended March 31, 1998.

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 March 31,
    1999 cash in the amount in aggregate of approximately $4.6 million, of which
    approximately $4.0 million was paid by Becton Dickinson and approximately
    $600,000 was paid by Nanogen. In addition, at March 31, 1999, approximately
    $2.6 million was due to the Partnership, of which approximately $2.0 million
    was due from Becton Dickinson and $660,000 was due from Nanogen. The amount
    due to the Partnership by Nanogen has been recorded as Nanogen's share of
    the joint venture's loss for the three months ended March 31, 1999. The
    General Partnership Agreement also contemplates additional research funding
    aggregating approximately $14.0 million, of which $4.3 million is to be paid
    by Nanogen, during the period from April 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 

                                                                              6
<PAGE>

    addition to the above-described payments, Becton Dickinson and Nanogen have 
    agreed to contribute additional amounts to fund marketing and manufacturing 
    startup.






                                                                              7
<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 March 31, 1999, had an accumulated deficit 
of approximately $54.3 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 months ended March 31, 1999, revenue from 
sponsored research totaled approximately $1.4 million, compared to 
approximately $885,000 for the three months ended March 31, 1998. 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 months ended March 31, 1999 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. For the three months ended March 31, 1998, sponsored 
research revenue was recognized in connection with our joint venture with 
Becton Dickinson and our research and development agreement with Aventis.

    Revenue from contracts and grants totaled approximately $577,000 for the 
three months ended March 31, 1999, compared to approximately $547,000 for the 
three months ended March 31, 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 months ended March 31, 1999 as compared to five 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 $6.9 million for the three months ended March 31, 
1999, from approximately $4.6 million for the three months ended March 31, 
1998. Research and development expenses include salaries, lab supplies, 
consulting, travel, facilities, 

                                                                              8
<PAGE>

product design and prototype development, and other expenditures relating to 
research and product development. The increase in research and development 
expenditures in the first quarter of 1999, compared to the first quarter of 
1998, can be primarily attributed to costs associated with the development 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 $1.8 million for the three months ended March 31, 1999, 
compared to approximately $1.5 million for the three months ended March 31, 
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 three 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 quarter ended March 31, 1998,

    INTEREST INCOME (EXPENSE), NET. The Company had net interest income of 
approximately $568,000 for the three months ended March 31, 1999, compared to 
net interest income of approximately $159,000 for the three months ended 
March 31, 1998. The significant increase in interest income can be attributed 
to larger cash balances resulting from net proceeds received upon the 
completion of our initial public offering and concurrent private placement of 
equity securities in April 1998. The increase in interest income was 
partially offset by higher interest expense during the three months ended 
March 31, 1999, due to greater amounts of equipment under capital leases in 
1999 than in 1998.

    EQUITY IN LOSS OF JOINT VENTURE. The Company recognized a loss of 
approximately $660,000 for the three months ended March 31, 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 months ended March 31, 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.

    To date we have funded most of our equipment acquisitions and leasehold 
improvements through capital leasing facilities. During the first quarter of 
1999, we received proceeds from equipment financing of approximately 
$395,000. This compares to $1.6 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. 

                                                                              9
<PAGE>

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 $5.3 million and 
$3.2 million for the three months ended March 31, 1999 and 1998, 
respectively. Cash used for operations was primarily related to costs 
associated with the support of our expanding operations, including higher 
personnel costs, product development costs, and legal fees relating to 
establishing and maintaining our intellectual property rights.

    At March 31, 1999, we had approximately $55.8 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 
conducting an assessment of our computer systems, software applications, 
equipment and outside vendors and suppliers to identify which systems may be 
impacted by Year 2000 issues. We are making appropriate modifications and 
updates to internal information systems, some of which have been or are being 
done in the ordinary course of business. Our goal is to ensure, to the extent 
possible, that the transition from the year 1999 to the year 2000 will not 
have a materially adverse impact on operational, research or administrative 
capabilities. After completing the assessment process, we will develop a 
corporate-wide comprehensive strategy to address the problems associated with 
the Year 2000 transition. It is expected that this strategy will continually 
evolve as new issues arise and old ones disappear.

    We are in the process of assessing and initiating formal communications 
with our current partners and third party suppliers of products and services, 
including third parties with whom we have material relationships, in an 
effort to obtain written certification of their compliance to the Year 2000 
issue. We intend to develop an action list, as well as contingency plans 
based on the assessment of each third party's response to the Year 2000 
issue. In the event any such third party cannot timely provide us with 
products, services, or continue collaborations with us, our results of 
operations could be adversely affected. For example, our research and 
development efforts could be interrupted resulting in delays in meeting our 
obligations to existing collaborations, delays in progress of our product 
development and, consequently, delays in attracting new collaborative 
partners.

                                                                              10
<PAGE>

    Based upon a preliminary review of our systems, we estimate that the 
total cost of achieving Year 2000 readiness for our internal systems and 
equipment will be less than $150,000.

    Since no significant issues have arisen based on our preliminary 
assessments, we have not yet developed a contingency plan to address any 
material Year 2000 issues. A contingency plan, if required, will be developed 
immediately upon completion of our assessment. While we continue to believe 
that the Year 2000 matters discussed above will not have a materially adverse 
impact on our business, financial condition or results of operations, it is 
not possible to determine with certainty whether or to what extent we may be 
affected. We have not yet developed a reasonably likely worst case scenario 
with respect to Year 2000 problems we may encounter.

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, Hoechst (through a 
subsidiary) and Elan that contemplate the commercialization of products 
resulting from research and development collaboration agreements between the 
parties. These collaborations may not be successful.

                                                                              11
<PAGE>

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

    At March 31, 1999, we had an accumulated deficit of approximately $54.3 
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.

                                                                              12
<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. We may 
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.

                                                                              13
<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.

                                                                              14
<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 

                                                                              15
<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.













                                                                              16
<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 was 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:

<TABLE>
<S>                                                    <C>
               Repayment of indebtedness               $  1,753,000
               Working capital                         $ 20,550,000
               Temporary investments                   $ 16,397,000
</TABLE>

          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 6.  EXHIBITS AND REPORTS ON FORM 8-K

     (a)  Exhibits

          27.1    Financial Data Schedule.

     (b)  Reports on Form 8-K

          No Reports on Form 8-K were filed during the three months ended 
          March 31, 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          MAY 13, 1999              /s/ HOWARD C. BIRNDORF
              ------------------------       ----------------------------------
                                             HOWARD C. BIRNDORF
                                             CHAIRMAN OF THE BOARD AND CHIEF
                                             EXECUTIVE OFFICER
                                             (PRINCIPAL EXECUTIVE OFFICER)



      DATE          MAY 13, 1999              /s/ DANIEL D. BURGESS
              ------------------------       ----------------------------------
                                             DANIEL D. BURGESS
                                             VICE PRESIDENT, CHIEF FINANCIAL
                                             OFFICER
                                             (PRINCIPAL FINANCIAL OFFICER)




<PAGE>

                                  NANOGEN, INC.
                                  EXHIBIT INDEX

<TABLE>
<CAPTION>

EXHIBIT NO.                         DESCRIPTION                               PAGE
<S>         <C>                                                               <C>
27.1        Financial Data Schedule.............................................20

</TABLE>