<PAGE>

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

                                   FORM 10-K
                                 -------------


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

                  FOR THE FISCAL PERIOD ENDED DECEMBER 31, 1998

                                       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)

       REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (619) 546-7700

           Securities registered pursuant to Section 12(b) of the Act:
                                      NONE
           Securities registered pursuant to Section 12(g) of the Act:
                          Common Stock $.001 par value
                         Preferred Stock Purchase Rights
                                (Title of Class)

  Indicate by check mark whether the registrant (1) has filed all reports
  required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
  1934 during the preceding 12 months (or for such shorter period that the
  registrant was required to file such reports), and (2) has been subject to
  such filing requirements for the past 90 days.

                          YES     X            NO
                               -------             -------

  Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
  of Regulation S-K (Section 229.405 of this chapter) is not contained herein,
  and will not be contained, to the best of registrant's knowledge, in
  definitive proxy or information statements incorporated by reference in Part
  III of this Form 10-K or any amendment to this Form 10-K. [ ]

<PAGE>

  The aggregate market value of the voting stock held by non-affiliates of the
  registrant based upon the closing sale price of the Common Stock on March 24,
  1999, as reported on the Nasdaq National Market was approximately
  $109,464,453. Shares of Common Stock held by each executive officer and
  director and by each person who owns 10 percent or more of the outstanding
  Common Stock have been excluded in such calculation as such persons may be
  deemed to be affiliates. This determination of affiliate status is not
  necessarily a conclusive determination for other purposes.

  The number of shares outstanding of the registrant's common stock was
18,834,207 as of March 24, 1999.



                       DOCUMENTS INCORPORATED BY REFERENCE

REGISTRANT'S PROXY STATEMENT TO BE FILED WITH THE SECURITIES AND EXCHANGE
COMMISSION IN CONNECTION WITH THE SOLICITATION OF PROXIES FOR THE REGISTRANT'S
1999 ANNUAL STOCKHOLDER'S MEETING TO BE HELD ON JUNE 30, 1999 IS INCORPORATED BY
REFERENCE IN PART III, ITEM 10 (AS TO DIRECTORS), 11, 12 AND 13 OF THIS FORM
10-K.



<PAGE>

                                                NANOGEN, INC.
                                                  FORM 10-K
                                                    INDEX

<TABLE>
<CAPTION>
                                                                                                   PAGE
                                                                                                   ----
                                               PART I
<S>               <C>                                                                              <C>
Item 1.           Business.......................................................................... 1

Item 2.           Properties........................................................................18

Item 3.           Legal Proceedings.................................................................18

Item 4.           Submission of Matters to a Vote of Security Holders...............................19

                                               PART II

Item 5.           Market for Registrant's Common Equity and Related Stockholder Matters.............19

Item 6.           Selected Financial Data...........................................................20

Item 7.           Management's Discussion and Analysis of Financial Condition
                    and Results of Operations.......................................................21

Item 7A.          Quantitative and Qualitative Disclosures About
                    Market Risk.....................................................................24

Item 8.           Financial Statements and Supplementary Data.......................................24

Item 9.           Change in and Disagreements with Accountants on Accounting and
                    and Financial Disclosures.......................................................24

                                               PART III

Item 10.          Directors and Executive Officers of the Registrant................................25

Item 11.          Executive Compensation............................................................25

Item 12.          Security Ownership of Certain Beneficial Owners and Management....................25

Item 13.          Certain Relationships and Related Transactions....................................25

                                               PART IV

Item 14.          Exhibits, Financial Statement Schedules, and Reports on Form 8-K..................25


SIGNATURES..........................................................................................28

</TABLE>

<PAGE>



                                     PART I

ITEM 1.  BUSINESS

OVERVIEW

    We integrate advanced microelectronics and molecular biology into a 
platform technology with potential commercial applications in the biological 
fields of biomedical research, diagnostics, drug discovery, forensics, 
agriculture, and environmental testing. Our technology may also have 
applications in the electronics and telecommunications industries. We are 
developing an automated system which incorporates a proprietary semiconductor 
microchip and may provide a flexible tool for the rapid identification and 
analysis of test samples containing charged molecules.

    Through the use of microelectronics, our technology enables the active 
movement and concentration of charged molecules to and from designated 
microlocations, or test sites, on the semiconductor microchip. This 
electronic concentration of molecules greatly accelerates molecular binding 
at each microlocation. In addition, our technology allows the simultaneous 
analysis of multiple test results from a single sample.

    The open architecture design of our system enables us to offer microchips 
with arrays designed for specific applications or with arrays that can be 
customized by the end user. We plan to introduce our first product to 
selected customers in the biomedical research market in late 1999.

    Because of the importance of the biomedical research market as a 
beachhead, we anticipate being directly involved with marketing our first 
product line to this segment of our business. For follow-on applications, we 
anticipate partnering with companies which can bring infrastructure, 
expertise and a customer base to a particular application, allowing us to 
focus our resources on product development.

     We have established corporate alliances in infectious disease 
diagnostics, drug discovery and genomics. We are developing products to 
expedite the diagnosis of infectious disease through our joint venture with 
Becton, Dickinson and Company ("Becton Dickinson"). We have also entered into 
a collaboration with Aventis Research and Technologies (an affiliate of 
Hoechst AG) ("Aventis") to develop drug discovery tools, and a collaboration 
with Elan Corporation, plc ("Elan"), for genomic applications. Our 
collaborations permit integration of our technology with the resources and 
technology of our partners, while allowing us to independently pursue 
diagnostics, drug discovery and genomics opportunities outside the scope of 
these collaborations.

OUR PLATFORM TECHNOLOGY

     Our proprietary platform technology takes advantage of the fact that 
most biological molecules are either positively or negatively charged. 
Through the use of microelectronics, this technology enables the active 
movement and concentration of electronically charged molecules to and from 
designated test sites on a semiconductor microchip. These test sites are 
arranged in an array on our proprietary microchips. In addition, the 
technology allows for the simultaneous analysis of multiple test results, or 
"multiplexing," from a single sample. We believe these attributes make our 
technology well suited to unraveling complex genetic information.

    We believe our proprietary technology has applications for the analysis 
of any unknown charged biological molecule which is capable of binding 
specifically to a known capture molecule on a microchip. We have initially 
focused on DNA-based sample analysis in developing applications utilizing our 
platform.

    Our technology allows small sequences of DNA capture probes to be 
electronically placed at, or "addressed" to, specific sites on the microchip. 
A test sample can then be analyzed for the presence of target DNA molecules 
by determining which of the DNA capture probes on the array bind, or 
hybridize, with complementary DNA in the test sample. In contrast to 
nonelectronic or passive hybridization with conventional arrays on paper or 
glass "chips," the use of electronically mediated active hybridization to 
move and concentrate target DNA molecules accelerates hybridization. 
Electronically mediated hybridization occurs in minutes rather than the hours 
required for passive hybridization techniques.


                                        1
<PAGE>

    In addition to DNA applications, we believe our technology may be 
applicable to a number of other analyses, including antigen-antibody, 
enzyme-substrate, cell-receptor, and cell separation techniques.

    Our system can integrate in a single platform the following electronic 
operational features:

    ELECTRONIC ADDRESSING. Electronic addressing is the process by which we 
place charged molecules at specific test sites. Since DNA has a strong 
negative charge, it can be electronically moved to an area of positive 
charge. A test site or a row of test sites on the microchip is electronically 
activated with a positive charge. A solution of DNA probes is introduced onto 
the microchip. The negatively charged probes rapidly move to the positively 
charged sites, where they concentrate and are chemically bound to that site. 
The microchip is then washed and another solution of distinct DNA probes can 
be added. Site by site, row by row, an array of specifically bound DNA probes 
can be addressed on the microchip. Multiplexed sites can be addressed 
simultaneously allowing for speed and flexibility of array assembly. With the 
ability to electronically address capture probes to specific sites, the 
Nanogen system allows end users to build custom arrays through the placement 
of specific capture probes on a microchip. These microchip arrays may provide 
research professionals with a powerful and versatile tool to process and 
analyze molecular information.

    ELECTRONIC CONCENTRATION AND HYBRIDIZATION. Following electronic 
addressing, we use electronics to move and concentrate target molecules to 
one or more test sites on the microchip. The electronic concentration of 
sample DNA at each test site promotes rapid hybridization of sample DNA with 
complementary capture probes. In contrast to the passive hybridization 
process, the electronic concentration process has the advantage of 
significantly accelerating the rate of hybridization of a given target 
molecule.

    ELECTRONIC STRINGENCY CONTROL. Electronic stringency control provides a 
means to quickly and easily remove non-complementary DNA as part of the 
hybridization process. Electronic stringency provides quality control for the 
hybridization process and ensures that any bound pairs of DNA are truly 
complementary. The precision, control, and accuracy of our platform 
technology, through the use of the controlled delivery of current in the 
electronic stringency process may permit the detection of single point 
mutations, single base pair mismatches or other genetic mutations which have 
significant implications in a number of disease states. Electronic 
manipulation allows rapid and selective stringency conditions to be applied 
to individual test sites, which cannot be achieved with conventional methods. 
In contrast to conventional approaches, our technology can also accommodate 
both short and long single-stranded fragments of DNA on the same chip. This 
flexibility reduces the required number of probes and related test sites on 
the microchip. Currently marketed DNA arrays are difficult to control, 
require more uniformity in the sample and require greater replication of 
possible base pair mismatches.

    ELECTRONIC MULTIPLEXING. Our electronic multiplexing feature allows the 
simultaneous analysis of multiple tests from a single sample or multiple 
samples to be queried for a limited number of tests. Electronic multiplexing 
is facilitated by the ability to control individual test sites (for 
addressing of capture probes and concentration of test sample molecules) 
which allows for the simultaneous use of biochemically unrelated molecules on 
the same microchip. Sites on a conventional DNA array cannot be individually 
controlled, and therefore the same process steps must be performed on the 
entire array. The use of electronics in our technology provides increased 
versatility and flexibility over these conventional methods.

    STRAND DISPLACEMENT AMPLIFICATION. Strand Displacement Amplification 
("SDA") is a proprietary target amplification process whereby very low 
numbers of diagnostic targets in a test sample are enzymatically amplified to 
exponentially higher levels, greatly simplifying accurate detection of these 
targets. Because this process does not require cycling of temperatures, it is 
extremely fast, and complex instrumentation is not required. Our joint 
venture with Becton Dickinson was granted non-exclusive rights to Becton 
Dickinson's patents relating to SDA in infectious disease diagnostics. In 
addition, we were granted nonexclusive rights to use SDA in the fields of IN 
VITRO human genetic testing and cancer diagnostics. We believe that SDA may 
be an important element in the development of sample-to-answer applications 
for our technology platform.

OUR SYSTEM'S COMPONENTS

    Our system consists of both a disposable cartridge containing a 
proprietary semiconductor microchip and a fully automated instrument that 
controls all aspects of microchip operations, processing, detection and 
reporting. The 


                                        2
<PAGE>

system has been designed so that the operator inserts a disposable cartridge 
containing a test sample into the instrument. All subsequent steps are 
handled automatically under computer control. We have also developed a 
benchtop microchip loader for those researchers wishing to electronically 
address microchips with their own capture probes.

DISPOSABLE CARTRIDGE

    The disposable cartridge consists of a proprietary semiconductor 
microchip with electrical and fluidic connections to the instrument. We are 
finalizing designs for manufacturing commercial cartridges based on 
successful tests with a number of prototype cartridges. We expect that the 
disposable cartridge and microchip can be manufactured in high volumes at a 
low cost relative to current technologies.

    SEMICONDUCTOR MICROCHIP. Our proprietary microchip capitalizes on 
advances in the semiconductor industry and is designed and constructed using 
microlithography and fabrication techniques. Our microchip is coated with a 
proprietary permeation layer to which capture probes are attached and is 
mounted on the disposable cartridge. We have developed arrays of various 
sizes utilizing both passive and active CMOS microchips, as well as flip chip 
assembly technologies. We expect our initial commercial cartridges to employ 
100 different test sites.

    We are aware of U.S. and corresponding foreign patents and applications 
which are assigned to Affymax Technologies, N.V., and which relate to devices 
having 1,000 or more groups of oligonucleotides occupying a total area of 
less than 1 cm2 on a substrate. In the event that we proceed with the 
development of arrays with more than 1,000 groups of oligonucleotides, we 
expect to design our microchips through, among other things, the selection of 
the physical dimensions and methods of binding so as to avoid infringing 
these patents.

    PERMEATION LAYER. Our proprietary permeation layer, which is critical to 
the proper functioning of our system, is the interface between the surface of 
the microchip and the biological test environment. The permeation layer 
isolates the biological materials from the harsh electrochemical environment 
near the electrode surface and provides the chemistry necessary for 
attachment of capture probes.

    CAPTURE PROBES. Capture probes or other capture molecules are 
electronically addressed to the desired microlocations and chemically 
attached to the permeation layer. Because independent control can be applied 
at any test site on our microchip, different capture probes can be addressed 
on the same microchip, allowing multiple tests to be processed 
simultaneously. Our cartridges can be sold with preloaded sets of capture 
probes or can be customized by the end user in "build-your-own-chip" 
applications which will allow the customer to assemble specific probes onto a 
microchip to perform individualized analyses.

OUR INSTRUMENT

    Our fully integrated instrument system consists of four major subsystems: 
(1) a highly sensitive, laser-based fluorescence scanner that detects 
molecular binding, (2) a fluid handling subsystem that controls test sample 
application and washing steps, (3) computer hardware and software that allow 
the operator to select assays from a graphical user menu which controls all 
microchip operations, tabulates test results and prints test reports, and (4) 
a separate freestanding microchip loader to perform electronic addressing of 
blank microchips.

    FLUORESCENT ARRAY SCANNER. The fluorescent scanner uses pattern 
recognition techniques and optoelectronic technology to reduce instrument 
cost and size and eliminate the need for complicated array positioning 
mechanics. In its present configuration, the scanner is able to perform high 
sensitivity scans of 100 test site arrays in less than two minutes.

    FLUIDICS STATION. The instrument automates the movement of the reagents 
and test sample onto the disposable cartridge. The fluidic subassembly of the 
instrument includes a panel of precision syringe pumps, a cartridge-mounted 
sample assembly and fluidic connections between the instrument and the 
disposable cartridge.

    COMPUTER HARDWARE AND SOFTWARE SYSTEM. A multi-tasking operating system 
and microprocessor control all aspects of machine operation, including 
bar-coded assay selection, assay operation, fluorescent signal detection and 
signal processing, calculation of assay results and report generation. Each 
of the individual array locations is 


                                        3
<PAGE>

separately controlled by the microprocessor. Fluorescent signals emanating 
from positive test sites are scanned, monitored and quantitated.

    MICROCHIP LOADER. For biomedical research applications, our system will 
include a cartridge/microchip loader that will allow the user to 
electronically address their own probes to test sites on up to four chips 
simultaneously. For the diagnostics market and most other applications, a 
loader will not be required because we intend to provide preaddressed 
microchips for specific panels of tests. Multiple loaders can operate 
concurrently under system control.

COMMERCIAL STRATEGY

    Our commercial strategy is to make our proprietary platform technology a 
standard for molecular identification and analysis across a broad range of 
applications. We expect our initial product to be a benchtop analysis system 
for use in biomedical research applications. The capabilities that are 
incorporated into this system will form the core technology platform that 
will serve as the basis for expanding into other biological and nonbiological 
areas.

    We believe that the speed and flexibility of "build-your-own-chip" 
features will be very attractive to researchers and will help drive further 
application development. Over time, it is expected that additional features, 
such as sample-to-answer capability and portability at reduced cost, may 
broaden the market potential from the research market to markets many times 
larger that include diagnostics, forensics, agriculture, drug discovery and 
environmental applications.

    We are seeking to use substantially the same core hardware and disposable 
cartridge platform across a spectrum of applications. By doing this, we 
believe we can establish our platform as an industry standard and also reduce 
development costs for follow-on applications. This approach should also allow 
us to achieve manufacturing economies of scale that may help reduce our cost 
of goods sold over time.

    Because of the importance of the research market as a beachhead, we 
anticipate being directly involved with marketing our first product line to 
this segment of our business. For follow-on applications, we anticipate 
partnering with companies that can bring infrastructure, expertise and a 
customer base to a particular application, allowing us to focus our resources 
on product development.

    Examples of this strategy are Nanogen's relationships with Becton 
Dickinson in infectious disease diagnostics and Aventis in drug discovery. In 
both of these relationships, we are partnering with recognized experts in 
their fields in such a way that we receive development funding, sales and 
marketing expertise, as well as a significant portion of the potential 
downstream profits.

    We may enter into similar arrangements with other companies for 
additional applications, as well as continue using grant resources to help 
offset further development expenditures.

PRODUCTS AND APPLICATIONS UNDER DEVELOPMENT

BIOMEDICAL RESEARCH APPLICATIONS

    Worldwide genomics efforts, including the Human Genome Project and other 
public and private genetic sequencing efforts, are actively identifying and 
sequencing genes of many organisms. As these genes and their nucleotide 
sequences are identified, additional research will focus on how the genome, 
the genetic content of the cell, controls and influences biological function. 
Gene expression studies are often used to elucidate which of the genes 
contained within the genome are regulated during disease or in response to a 
variety of stimuli. Such studies also determine how specific mutations in a 
gene affect the normal expression and operation of that gene. This basic 
understanding may allow the development of new diagnostic and therapeutic 
approaches to a disease, according to its genetic profile.

    We expect to complete development of our first commercial product, a 
benchtop molecular analysis system, for use in the biomedical research 
market. Unlike the high density arrays and sequencing technologies now in the 
marketplace, our focus will be on targeted analysis of data from the genomics 
revolution--helping researchers 


                                        4
<PAGE>

define the function of genes rather than discover new genes. We believe our 
technology is well suited for this research, given the speed, user 
programmability, multiplexing capability and sensitivity of our unique 
platform. Our platform can also be used in conjunction with high throughput 
technologies, such as high density arrays and sequencers.

    Recent market research indicates that while researchers want to use high 
throughput devices to discover genes and genetic mutations, they will want to 
explore the function and impact of these genes and mutations with a more 
targeted technology such as that being developed by us. Given that 
researchers are just beginning to move beyond gene discovery into this 
targeted analysis area called functional genomics, the timing of our 
anticipated product introduction may be well suited to meet this evolving 
market need. Independent market research in this area has indicated that the 
market potential for targeted arrays like ours will grow rapidly from $80 
million in 1998 to almost $500 million by 2002.

    Our initial strategy for entering this market will be to focus on a small 
number of sophisticated commercial and academic users and provide technical 
support and applications specialists to assist this group of scientists in 
applying the technology. With these initial users, which we anticipate 
establishing in late 1999, we will conduct user group meetings to further 
identify and develop appropriate applications in this rapidly changing 
market. Our initial product offering is expected to include features such as 
the ability to perform assays on single nucleotide polymorphisms (SNPs), 
point mutations and genetic repeats in a multiplexed format using a variety 
of different methods.

    We plan to further define and develop additional capabilities, such as 
gene expression, on-chip amplification and sample processing. As these 
capabilities are added, we expect to start expanding our customer base to a 
wider group that may ultimately encompass a significant percentage of the 
biomedical research labs in the U.S. and other parts of the world.

DIAGNOSTICS APPLICATIONS

    INFECTIOUS DISEASES

    We are applying our technology in infectious disease diagnostics to 
develop automated tests to replace the manual and time-intensive procedures 
used in hospitals and reference laboratories. The role of the clinical 
microbiology laboratory is to detect, identify and determine antibiotic 
sensitivity of disease causing microorganisms. To accomplish this task, 
colonies of microorganisms from patient specimens are grown, or cultured, in 
various growth media. Following colony growth, various direct and indirect 
techniques are utilized to determine the identity and, as required, the 
sensitivity of the microorganism to specific antibiotics. Using currently 
available technologies, the entire process may take days or weeks to complete 
while the patient, requiring immediate therapy, must be treated by the 
clinician based upon the best clinical facts available at that time. Upon 
receipt of the diagnostic analysis from the laboratory, the initial patient 
treatment protocol may need to be modified in order to treat the patient more 
effectively.

    Current culture-based methods detect a single microorganism at one time. 
Because a particular infectious episode may be caused by one of many 
microorganisms or several microorganisms together, multiple tests may be 
required to determine the correct diagnosis. Our technology addresses these 
shortcomings by allowing the simultaneous analysis of multiple microorganisms 
from a single patient sample. We believe our technology and integrated system 
may speed the time-to-result for diagnostic tests and patient treatment and 
offer our customers the opportunity to lower their costs and improve 
productivity by automating all or a significant portion of their 
labor-intensive testing.

    Through our joint venture with Becton Dickinson, we are developing a 
platform which is applicable to a potentially broad range of products 
relating to the detection of infectious disease and the analysis of 
antibiotic resistance, each of which may incorporate Becton Dickinson's 
proprietary SDA technology. To date, our joint venture with Becton Dickinson 
has achieved all of its product development milestones. The joint venture 
contemplates that Becton Dickinson will market any infectious disease 
products developed by the joint venture and that profits will be split 
equally by the parties once capital contributions have been reimbursed.


                                        5
<PAGE>

    PHARMACOGENOMICS

    We believe that the ability of our technology to screen simultaneously 
for various DNA sequences and the ability to differentiate between single 
base pair mismatches has potentially wide applicability to the field of 
genetic testing in general and pharmacogenomics in particular. The principle 
behind pharmacogenomics is that patients with one kind of genetic profile 
will react differently to a given drug than a different group of patients 
with a slightly altered genetic makeup. The goal of pharmacogenomics would be 
for physicians to be able to prescribe the appropriate medicine for a 
particular patient that would maximize efficacy and minimize side effects 
based on that patient's genetic profile.

    With our technology, the opportunity exists for pharmaceutical and 
biotechnology companies to use our initial benchtop system to identify 
important genetic variations early in the drug development process, to use a 
portable version of the system during clinical trials to help stratify 
patients and identify those receiving the maximum benefit from treatment; 
and, ultimately, to develop a small sample-to-answer, FDA-approved diagnostic 
test that can be used in a doctor's office potentially while a patient is 
waiting. We believe the potential to be able to provide this bridge from the 
research environment through to a portable diagnostic system may be important 
in the area of pharmacogenomics. We have active development programs underway 
to develop both the benchtop and portable version of the system that would be 
required for this market.

    OTHER GENETIC TESTING APPLICATIONS

    As the Human Genome Project and other public and private genetic 
sequencing efforts yield increasing amounts of genetic information, the 
demand for genetic predisposition testing will continue to grow. The 
combination of novel therapeutic approaches, such as gene therapy, and the 
discovery of new genes could lead to earlier and more precise diagnosis and 
more refined therapeutic interventions.

    Because many important genetic diseases are ideally suited to diagnosis 
in multiplexed arrays, we believe that our technology platform could 
contribute significantly to the expansion of testing in this area. For 
example, in cancer diagnostics, certain mutations are indicative of a 
predisposition to certain types of cancer. Because many diseases involve 
multiple mutations, the ability to analyze all possible mutations has 
previously been expensive and impracticable. Our electronic stringency 
control feature potentially permits rapid and accurate testing for these 
single point mutations. While our development efforts in this area with 
respect to specific genetic tests are still at an early stage, our core 
technology platform for other diagnostic applications may be well suited for 
these opportunities.

DRUG DISCOVERY APPLICATIONS

    We believe we have a powerful tool which will elucidate appropriate 
pathways for therapeutic intervention, identify and evaluate lead compounds 
and simultaneously assess the efficacy and toxicology of these compounds in 
model systems. It is estimated that the preclinical drug discovery process 
takes an average of six and one-half years. Consequently, we believe there is 
a significant demand for improved tools which accelerate the drug discovery 
process.

    We believe the microelectronic array format and independent test site 
control of our system are well suited for applications in drug discovery. Our 
electronic technology is expected to enable the rapid manipulation of 
potential drug molecules against targets such as bacteria, virus, tumor or 
immune response cells addressed to the microchip to determine drug efficacy, 
thus simplifying the drug discovery process. The combination of electronic 
addressing and the electronic protection of specific areas of the microchip 
allows the targeting of chemical building blocks to unique locations on the 
array. We believe our system may provide an efficient automated method for 
drug lead optimization.

    To further advance our efforts in this area, we have entered into a 
research and development collaboration with Aventis. As part of our 
collaboration with Aventis, Nanogen is working on a novel electronic 
combinatorial approach toward drug screening and discovery by combining 
technologies from both companies. Nanogen and Aventis met all of the 
milestones for the collaboration in 1998, agreed to extend the research 
program from two to three years and are now in discussions about how to best 
commercialize this product opportunity.


                                        6
<PAGE>

EMERGING BIOLOGICAL MARKETS

    The market potential for our semiconductor microchip technology beyond 
these initial areas is significant. Such applications include biological 
applications in the areas of forensics, agriculture, veterinary and 
environmental testing. We believe the core technology platform we are 
developing may be readily adaptable to these markets, and we have already 
been approached by a number of companies active in these areas about 
opportunities for collaboration.

NANOTRONICS:  NONBIOLOGICAL APPLICATIONS

    Rapid advances in the microelectronics industry in the last several 
decades have led to the development of integrated circuits which are smaller 
and far more complex than would have been envisioned twenty years ago. If 
this pace of change is to continue, new manufacturing tools and processes 
will need to be developed. These new techniques will need to be able to 
direct the placement of micro and nanoscale components precisely onto 
increasingly small and densely packed surfaces. We believe one of the 
opportunities to do this is by combining what nature has already developed--a 
molecular biology approach--with our knowledge of how to move and manipulate 
materials and devices using electronic fields.

    We acquired Nanotronics in January 1998 to apply our core 
microelectronics biochip technology to potential applications in 
nonbiological areas which include nanofabrication and molecular electronics. 
Based on the intrinsic self-assembly and programmable qualities of DNA, the 
Nanotronics technology uses DNA to direct the heterogeneous integration of a 
number of molecular and nonmolecular components onto a microelectronic chip. 
Presently, there are a number of academic groups, government research labs, 
and electronics companies involved in the development of molecular electronic 
components, but no one has successfully developed a way to integrate them 
into useful devices. Our integrated "host substrate" or "motherboard" array 
capability could serve to provide useful new tools with the ability to take 
advantage of these valuable components.

    Nanotronics' powerful electronic "pick and place" array technology has 
several advantages compared to the more difficult conventional heterogeneous 
integration processes. This Nanotronics technology could incorporate 
components ranging in size from molecular scale to micron scale, something 
traditional microelectronic methods cannot achieve. Also, using electric 
field specificity control, we may have the ability to form novel integrated 
devices in a more timely and cost-effective fashion. Nanotronics is working 
to expand the capabilities of its technology base for application in a number 
of areas.

    For example, Nanotronics is evaluating the use of its platform technology 
to facilitate the heterogeneous integration of various microfabricated 
"lift-off" components like lasers and diodes, for the development of new 
photonic or electronic devices. Other applications could include analog and 
digital cell phone circuit improvements and development of new electronic 
laboratory testing systems.

    In addition, in 1998 we received several core patents for the use of our 
technology in the area of optical memory. These patents have already led to 
inquiries from third parties interested in significantly expanding the memory 
storage capacity of optical memory devices.

COLLABORATIVE ALLIANCES

    We have established collaborative alliances in the areas of infectious 
disease diagnostics, drug discovery and genomics as part of our strategy to 
expand the applications and accelerate the commercialization of products 
derived from our technology. We are developing products to expedite the 
diagnosis of infectious disease through our joint venture with Becton 
Dickinson. We have also entered into a research and development collaboration 
and are discussing the establishment of arrangements with Aventis to 
commercialize drug discovery tools. We also have entered into a research and 
development agreement with Elan for genomics applications.

BECTON DICKINSON

    The Nanogen/Becton Dickinson Partnership, a Delaware general partnership
formed in October 1997 (the "Partnership") is seeking to develop and
commercialize products in the field of IN VITRO nucleic acid-based diagnostic


                                        7
<PAGE>

and monitoring technologies in infectious diseases. The products will be 
based on our proprietary semiconductor technology and Becton Dickinson's 
proprietary SDA technology. NanoVenture LLC, a Delaware limited liability 
company wholly-owned by Nanogen ("NanoVenture"), and Becton Dickinson Venture 
LLC, a Delaware limited liability company wholly-owned by Becton Dickinson 
("Becton Dickinson Venture"), are the general partners of the Partnership 
with (1) losses generally allocated in proportion to cash funding, (2) 
profits generally shared equally, and (3) distributions allocated 60 percent 
to Becton Dickinson Venture and 40 percent to NanoVenture until unrecovered 
partner cash contributions are equalized and thereafter distributions shared 
equally. The Master Agreement also contemplates that each of the parties will 
negotiate in good faith additional agreements with the Partnership in 
furtherance of the Partnership's business, including license agreements, 
manufacturing agreements, and marketing agreements. Pursuant to the Master 
Agreement, we granted to Becton Dickinson Venture, acting on behalf of the 
Partnership, a right of first offer to negotiate licenses in additional 
fields.

    Contributions for use in the research programs of approximately $4.6 
million have been paid to the Partnership through December 31, 1998, of which 
approximately $4.0 million was paid by Becton Dickinson and approximately 
$600,000 was paid by us. The General Partnership Agreement also contemplates 
additional research funding aggregating approximately $17.7 million during 
the period from January 1, 1999 through April 1, 2001 conditioned upon the 
achievement of milestones to be agreed upon by the partners. Of this amount, 
$12.5 million is expected to be paid by Becton Dickinson and $5.2 million is 
expected to be paid by us.

    In addition to funding research and development, we and Becton Dickinson 
have agreed to contribute additional amounts to fund marketing and 
manufacturing of products commercialized by the Partnership. The success of 
the Partnership will be dependent to a significant degree upon a mutuality of 
interest between Nanogen and Becton Dickinson. Becton Dickinson is a large 
company with other opportunities competing for its resources. Becton 
Dickinson may not make further capital contributions or allocate sufficient 
management or other resources to the Partnership to complete the development, 
manufacturing and marketing of Partnership products.

    The Partnership entered into a Collaborative Research and Development and 
License Agreement with us and Becton Dickinson, under which each company 
granted to the Partnership intellectual property and patent rights and 
conducts research and development activities.

    Concurrently with the execution of the joint venture, we entered into a 
worldwide, royalty-bearing, nonexclusive License Agreement with Becton 
Dickinson, relating to Becton Dickinson's proprietary SDA technology for use 
by us outside the Partnership in the fields of IN VITRO human genetic testing 
and IN VITRO cancer diagnostics.

    Failure by the Partnership to agree on and achieve milestones could 
result in termination of the Collaborative Agreement and the joint venture 
and dissolution of the Partnership. Agreed upon milestones may not be 
achieved in a timely fashion, if at all. The failure to agree on and achieve 
these milestones could have a material adverse effect on our business, 
financial condition and results of operations.

AVENTIS

    In December 1997, we entered into a Letter Agreement with Aventis, for an 
exclusive research and development collaboration relating to new drug 
discovery tools and immunodiagnostics research and the establishment of a 
joint venture. The arrangements for the commercialization of products, if 
any, developed as a result of the collaboration will be negotiated by the 
parties prior to completion of the research and development phase.

    In connection with the Letter Agreement, the parties entered into a 
definitive Collaborative Research and Development Agreement with an effective 
date of January 1, 1998. This Research and Development agreement includes 
three years of guaranteed research and development funding from the effective 
date. Under the agreement each party performs aspects of the research, with 
funding provided primarily by Aventis. The Letter Agreement and Research and 
Development Agreement contemplate the formation of a joint venture or other 
joint relationship to facilitate the commercialization of any products 
resulting from the collaboration.

    As part of our collaboration, we have agreed to issue a warrant for 
approximately 120,000 shares of Common Stock to Aventis at an exercise price 
of $8.75 per share. We have also agreed to issue to Aventis, upon the 
achievement of certain milestones, warrants to purchase up to approximately 
360,000 additional shares of Common 


                                        8
<PAGE>

Stock as follows: upon announcement by the parties of entry into the product 
development phase of the research and development collaboration, a warrant 
for the purchase of approximately 180,000 shares of Common Stock at a 50 
percent premium to the market price on the date of such entry, and upon the 
first commercial sale by the joint venture or other joint relationship, a 
warrant to purchase an additional 180,000 shares of Common Stock at a 50 
percent premium to the market price on the date of such sale. The warrants 
will have five-year maximum terms, provided that with respect to each such 
warrant issuance, if at any time subsequent to the issuance of the warrant 
the price of our Common Stock exceeds the exercise price by 50 percent or 
more, Aventis must exercise such warrant no later than the end of its next 
fiscal year.

ELAN

    In December 1997, we entered into a nonexclusive research and development 
agreement with Elan for the development of genomics and gene expression 
research tools. The agreement contemplates that we will develop products for 
discrimination of sequence variations such as single nucleotide 
polymorphisms, allelic variations, genotyping, and mutation detection. We may 
also develop products for use in expression monitoring of RNA levels for use 
in gene discovery, drug discovery, target validation, animal studies, and 
toxicity studies. We are currently discussing with Elan the conversion of 
this relationship into a Technology Development Program under which Elan and 
potentially other companies would gain early access to our technology in 
exchange for an up-front payment and additional payments to be made over time.

RESEARCH GRANTS

    We have a number of active research grants and contracts administered by 
various governmental agencies. In October 1998, we announced that we were 
awarded a contract by the Space and Naval Warfare Systems Center San Diego 
("SSC San Diego") for the Defense Advance Research Projects Agency and a 
grant from the National Institute of Justice ("NIJ") in amounts that could 
total approximately $8 million over a five-year period. The contract award 
which was made by SSC San Diego for the Defense Advance Research Projects 
Agency, includes over $2 million to be paid during the first two years, and 
options to extend the program for up to an additional three years that would 
pay us up to an additional $4.8 million. The goal of the program is to create 
an advanced miniaturized lab for biological warfare defense applications. We 
were also awarded an NIJ grant of $500,000. This was our second grant awarded 
under the U.S. Department of Justice, Office of Justice Programs to enable us 
to continue our work in the development of a portable microchip array-based 
genetic detector for rapid forensic DNA testing and identification at the 
crime scene.

RESEARCH AND PRODUCT DEVELOPMENT

    Our research and product development organization is dedicated to:

       -  Developing our DNA analysis platform,
       -  Using this basic technology in a number of different product areas,
       -  Planning system modifications for specific applications using a
          common platform, and
       -  Enhancing chip design and capabilities to simplify instrument
          design.

    We have project teams focused on technology applications for the research 
market, diagnostic applications for the Becton Dickinson collaboration, drug 
discovery applications for the Aventis collaboration and a genomics group 
supporting the Elan relationship. In addition, we have various groups 
supporting activities related to government contracts and grants for both 
biologic and nonbiologic applications.

PROPRIETARY TECHNOLOGY AND PATENTS

    We have eight issued U.S. patents, three foreign issued patents and a 
number of pending patent applications filed in the U.S. and abroad. Under a 
licensing agreement with Syntro Corporation, we obtained an exclusive license 
to U.S. Patent No. 4,787,963 relating to methods and means of annealing 
complementary nucleic molecules in exchange for payment of an initial fee, 
aggregate payments of $1 million during the agreement's first two years and 
the potential payment of certain royalties. In addition to pursuing patents 
and patent applications relating to our 


                                        9
<PAGE>

platform technology, we may enter into other license arrangements to obtain 
rights to third-party intellectual property where appropriate.

    Our or our licensors' patent applications may not issue. Issued patents 
may not be found valid if challenged. In addition, intellectual property 
rights licensed by us may not be successfully integrated into commercial 
products. Others may independently develop similar technologies or duplicate 
any technology developed by us. Because of the extensive time required for 
development, testing, and regulatory review of a potential product, it is 
possible that, before any of our products can be commercialized, any related 
patent may expire or remain in existence for only a short period following 
commercialization, thus reducing any advantage of the patent, which could 
adversely affect our ability to protect future product development and, 
consequently, our business, financial condition and results of operations.

    All of our inventions have originated in the U.S. and all patent 
applications were originally filed in the U.S. We also seek to protect these 
inventions through foreign counterpart applications filed in selected other 
countries. Because patent applications in the U.S. are maintained in secrecy 
until patents issue and since publication of discoveries in the scientific or 
patent literature often lag behind actual discoveries, we cannot be certain 
that we were the first to make the inventions covered by each of our issued 
or pending patent applications or that we were the first to file for 
protection of inventions set forth in such patent applications. Our planned 
or potential products may be covered by third-party patents or other 
intellectual property rights, in which case continued development and 
marketing of the products would require a license. Required licenses may not 
be available to us on acceptable terms, if at all. If we do not obtain these 
licenses, we could encounter delays in product introductions while we attempt 
to design around the patents, or could find that the development, manufacture 
or sale of products requiring these licenses is foreclosed.

    We are aware of U.S. and corresponding foreign patents and applications 
which are assigned to Affymax Technologies, N.V., and which relate to certain 
devices having 1,000 or more groups of oligonucleotides occupying a total 
area of less than 1 cm2 on a substrate. In the event that we proceed with the 
development of arrays with more than 1,000 groups of oligonucleotides, we 
expect to design our devices through, among other things, the selection of 
the physical dimensions and methods of binding to avoid infringing these 
patents. We are aware of U.S. and European patents and patent applications 
owned by Isis Innovations Ltd. (E. M. Southern). We have opposed one allowed 
European patent which had broad claims to array technology for analyzing a 
predetermined polynucleotide sequence. Isis Innovations' position with 
respect to the opposed patent is that the claims relate to what it terms the 
"diagnostic mode." Those claims have now all been narrowed to the point that 
if the claims are accepted by the European Patent Office, they would not be 
infringed by our technology. On May 5, 1998, The Opposition Division of the 
European Patent Office issued a provisional nonbinding opinion that the 
claims should be revoked. If the claims of the original European patent 
survive the opposition or if an application relating to arrays issues in 
another country with claims as broad as the original European patent, we 
would be subject to infringement claims that could delay or preclude sales of 
some or all of our anticipated diagnostic products.

    Litigation may be necessary to defend against or assert claims of 
infringement, to enforce patents issued to us, to protect trade secrets or 
know-how owned by us or to determine the scope and validity of the 
proprietary rights of others. In addition, interference proceedings declared 
by the USPTO may be necessary to determine the priority of inventions with 
respect to our patent applications. Litigation or interference proceedings 
could result in substantial costs to and diversion of our effort, and could 
have a material adverse effect on our business, financial condition, and 
results of operations. Any such efforts may not be successful.

    We may rely on trade secrets to protect our technology. Trade secrets are 
difficult to protect. We seek to protect our proprietary technology and 
processes by confidentiality agreements with our employees and certain 
consultants and contractors. These agreements may be breached, we may not 
have adequate remedies for any breach and our trade secrets may otherwise 
become known or be independently discovered by competitors. To the extent 
that our employees or our consultants or contractors use intellectual 
property owned by others in their work for us, disputes may also arise as to 
the rights in related or resulting know-how and inventions.


                                        10
<PAGE>

MANUFACTURING

    We design and then outsource semiconductor microchip fabrication, 
disposable cartridge components and instruments to third-party contract 
manufacturers. For microchips and cartridges, we perform many of the 
proprietary assembly steps in-house, including deposition of the permeation 
layer, placement of DNA capture probes and final electronic assembly and 
testing. We expect to enter into long-term manufacturing agreements with 
experienced third-parties for some or all of our commercial manufacturing 
needs for both instruments and cartridges. We believe our technology allows 
for large scale microchip production at a relatively low cost. We believe 
this scalability and low cost will help promote the rapid acceptance of our 
proprietary semiconductor-based platform technology as an industry standard. 
However, achieving these efficiencies will require substantial commercial 
volumes and there can be no assurance we will be successful in generating 
sufficient demand to scale up manufacturing capacity to levels that will 
allow our products to be priced competitively.

    We have limited experience in manufacturing as well as limited 
manufacturing capacity for our products, and as described above, we will be 
required to utilize third parties for some or all of our needs. There can be 
no assurance that we will be able to find third-party manufacturers with the 
skills required to manufacture our products successfully or on acceptable 
terms, if at all.

    If we or any of our contract manufacturers encounter future manufacturing 
difficulties, including problems involving the ability to scale up 
manufacturing capacity, production yields, quality control and quality 
assurance, or shortages of components or qualified personnel, it could have a 
material adverse effect on our business, financial condition and results of 
operations.

    Our and/or our third-party manufacturers will be required to comply with 
QSR requirements in order to produce products for sale in the United States 
and with applicable quality system standards and directives in order to 
produce products for sale in the European Union. Any failure by us or our 
contractors to comply with the QSR requirements or applicable European Union 
standards and directives may result in us or our contractors being required 
to take corrective actions, such as modification of our policies and 
procedures. Pending such corrective actions, we or our contractors could be 
unable to manufacture or ship any products, which could have a material 
adverse effect on our business, financial condition, and results of 
operation. Furthermore, our manufacturing facilities, and those of our 
third-party manufacturers, are subject to periodic inspection by regulatory 
authorities, and our operations must undergo QSR compliance inspections 
conducted by the FDA and corresponding state agencies. Additionally, prior to 
approval of a PMA, we and our third-party manufacturers' facilities, 
procedures, and practices will be subject to preapproval QSR inspection. 
Failure to pass such inspections may have a material adverse effect on our 
business, financial condition and results of operations.

COMPETITION

    As we develop applications of our technology, we expect to encounter 
intense competition from a number of companies that offer products competing 
in our targeted applications. We anticipate that our competitors in these 
areas will include health care companies that manufacture laboratory-based 
tests and analyzers, diagnostic and pharmaceutical companies, as well as 
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 development-stage companies that continue to 
enter these markets.

    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, 
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 making or developing products that 
compete with or will compete with any potential products of ours. There can 
be no assurance that our competitors will not succeed in developing or 
marketing technologies or products that are more effective or commercially 
attractive than our potential products, or that would render our technologies 
and products obsolete. Also, we may not have the financial resources, 
technical expertise or marketing, distribution or support capabilities to 
compete successfully in the future. Our success will depend in large part on 
our ability to maintain a competitive position with respect to our 
technologies. Rapid technological development by others may also result in 
competing products or technologies.


                                       11
<PAGE>

GOVERNMENT REGULATION

    We have not applied for FDA or other regulatory approvals with respect to 
any of our products under development. We anticipate the manufacturing, 
labeling, distribution and marketing of some or all of our diagnostic 
products will be subject to regulation in the U.S. and in other countries. In 
addition to clinical diagnostic markets, we also may pursue research, 
forensic, agricultural, environmental, laboratory and industrial applications 
for our products which may be subject to different government regulation. 
Aspects of our manufacturing and marketing activities may also be subject to 
federal, state and local regulation by various governmental authorities.

    In the U.S., the 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, and the regulations 
promulgated thereunder, the FDA regulates the preclinical and clinical 
testing, design manufacture, labeling, distribution and promotion of medical 
devices. We will not be able to commence marketing or commercial sales in the 
U.S. of new medical devices under development that fall within the FDA's 
jurisdiction until we receive clearance or approval from the FDA, which can 
be a lengthy, expensive, and uncertain process. Noncompliance with applicable 
requirements can result in, among other things, administrative 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, or criminal prosecution.

    In the U.S., medical devices are generally classified into one of three 
classes (I.E., Class I, II or III) on the basis of the controls deemed 
necessary by the FDA to reasonably ensure their safety and effectiveness. 
Class I devices are subject to general controls (E.G., labeling, premarket 
notification, and adherence to QSR). Class II devices are subject to general 
and special controls (E.G., performance standards, postmarket surveillance, 
patient registries and FDA guidelines). Generally, Class III devices are 
those which must receive premarket approval by the FDA to ensure their safety 
and effectiveness (E.G., life-sustaining, life-supporting, and implantable 
devices or new devices which have been found not to be substantially 
equivalent to a legally marketed devices). Before a new device can be 
introduced in the market, the manufacturer must generally obtain FDA 
clearance of a 510(k) notification or approval of a PMA application. Our 
products will vary significantly in the degree of regulatory approvals 
required. We believe that certain of our products for research, genomics, 
drug discovery and industrial applications will not require regulatory 
approvals or clearance. Some diagnostic products will require 510(k) 
approvals while other diagnostic and genetic testing products will require 
PMA approvals.

    A 510(k) clearance will generally only be granted if the information 
submitted to the FDA establishes that the device is "substantially 
equivalent" to a legally marketed predicate device. For any devices that are 
cleared through the 510(k) process, significant modifications or enhancements 
in the design or intended use that could significantly affect safety or 
effectiveness will require new 510(k) submissions. It generally takes from 
four to twelve months from submission to obtain 510(k) premarket clearance 
but the process may take longer.

    The PMA approval process is more expensive, uncertain, and lengthy than 
the 510(k) clearance process. A PMA must prove the safety and effectiveness 
of the device to the FDA's satisfaction, which typically requires extensive 
data, including but not limited to, technical, preclinical, clinical trials, 
manufacturing and labeling to demonstrate the safety and effectiveness of the 
device. Although clinical investigations of most devices are subject to the 
investigational device exemption requirements, clinical investigations of IN 
VITRO diagnostic tests, such as our products and products under development, 
are exempt from the investigational device exemption requirements, including 
the need to obtain the FDA's prior approval, provided the testing is 
noninvasive, does not require an invasive sampling procedure that presents a 
significant risk, does not intentionally introduce energy into the subject, 
and is not used as a diagnostic procedure without confirmation by another 
medically established test or procedure. In addition, the IN VITRO diagnostic 
tests must be labeled for research use only or investigational use only, and 
distribution controls must be established to assure that IVDs distributed for 
research or clinical investigation are used only for those purposes.

    The FDA may determine that we must adhere to the more costly, lengthy, 
and uncertain PMA approval process for our potential products. Significant 
modifications to the design, labeling or manufacturing process of an approved 
device may require approval by the FDA of a PMA supplement or a new PMA 
application.


                                        12
<PAGE>

    After a PMA is accepted for filing, the FDA begins its review of the 
submitted information, which generally takes between one and two years, but 
may take significantly longer. During this review period, the FDA may request 
additional information or clarification of information already provided. Also 
during the review period, an advisory panel of experts from outside the FDA 
will be convened to review and evaluate the application and provide 
recommendations to the FDA as to the approvability of the device. We may not 
be able to obtain necessary approvals on a timely basis, if at all, and 
delays in obtaining or failure to obtain such approvals, the loss of 
previously obtained approvals, or failure to comply with existing or future 
regulatory requirements could have a material adverse effect on our business, 
financial condition and results of operations.

    Manufacturers of medical devices for marketing in the U.S. are required 
to adhere to the QSR requirements (formerly Good Manufacturing Practices), 
which include testing, control and documentation requirements. Manufacturers 
must also comply with Medical Device Reporting requirements that a 
manufacturer report to the FDA any incident in which its product may have 
caused or contributed to a death or serious injury, or in which its product 
malfunctioned and would be likely to cause or contribute to a death or 
serious injury upon recurrence. Labeling and promotional activities are 
subject to scrutiny by the FDA and, in certain circumstances, by the Federal 
Trade Commission. FDA enforcement policy prohibits the marketing of approved 
medical devices for unapproved uses.

    We are subject to routine inspection by the FDA and certain state 
agencies for compliance with QSR requirements, medical device reporting 
requirements and other applicable regulations. The recently finalized QSR 
requirements include design controls that will likely increase the cost of 
compliance. We may incur significant costs to comply with laws and 
regulations in the future and these laws and regulations may have a material 
adverse effect upon our business, financial condition and results of 
operation.

    Any of our customers using our diagnostic devices for clinical use in the 
U.S. may be regulated under the Clinical Laboratory Improvement Amendments of 
1988 ("CLIA"). CLIA is intended to ensure the quality and reliability of 
clinical laboratories in the U.S. by mandating specific standards in the 
areas of personnel qualification, administration, participation in 
proficiency testing, patient test management, quality control, quality 
assurance and inspections. The regulations promulgated under CLIA establish 
three levels of diagnostic tests ("waived," "moderately complex" and "highly 
complex"), and the standards applicable to a clinical laboratory depend on 
the level of the tests it performs. CLIA requirements may prevent some 
clinical laboratories from using our diagnostic products. Therefore, CLIA 
regulations and future administrative interpretations of CLIA may have a 
material adverse impact on us by limiting the potential market for our 
products.

    The Food and Drug Administration Modernization Act of 1997 makes changes 
to the device provisions of the FD&C Act (the "Act") and other provisions in 
the Act affecting the regulation of devices. Among other things, the changes 
will affect the IDE, 510(k) and PMA processes, and also will affect device 
standards and data requirements, procedures relating to humanitarian and 
breakthrough devices, tracking and postmarket surveillance, accredited 
third-party review, and the dissemination of off-label information. We cannot 
predict how or when these changes will be implemented or what effect the 
changes will have on the regulation of our products. There can be no 
assurance that the new legislation will not impose additional costs or 
lengthen review times for our products.

    Additionally, our food pathogen products will be subject to the 
regulations of various domestic and foreign government agencies which 
regulate food safety and food adulteration, including the U.S. Department of 
Agriculture.

EMPLOYEES

    As of December 31, 1998, we had 132 full-time employees, of whom 49 hold 
Ph.D. or M.D. degrees and 14 hold other advanced degrees. None of our 
employees is covered by a collective bargaining agreement, and management 
considers relations with its employees to be good.


                                        13
<PAGE>

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.

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

    At December 31, 1998, we had an accumulated deficit of approximately $47 
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.


                                        14
<PAGE>

    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.

    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 


                                        15
<PAGE>

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.

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.


                                        16
<PAGE>

    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.

    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.


                                        17
<PAGE>

    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 2.  PROPERTIES

    We currently lease an approximately 45,000 square foot facility in San 
Diego, California, under a lease expiring in 2005. We have an option to renew 
the lease on this facility for two additional five-year terms. The facility 
currently houses our administrative offices and research and development 
laboratories, and is expected to be sufficient to meet our currently 
anticipated facilities needs at least through 1999.

ITEM 3.  LEGAL PROCEEDINGS

    There is no material litigation pending against us.


                                        18
<PAGE>

                                     PART II

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

    There were no matters submitted to a vote of security holders during the 
quarter ended December 31, 1998.

ITEM 5. MARKET FOR THE REGISTRANT'S COMMON EQUITY AND RELATED STOCKHOLDER
MATTERS

(a)      Changes in Securities

    On November 17, 1998, our Board of Directors adopted a Stockholder Rights 
Plan ("Rights Plan"). Under the terms of the Rights Plan, stockholders of 
record as of November 30, 1998 received a dividend of one Preferred Stock 
Purchase Right ("Right") for each share of common stock held on that date. If 
not earlier terminated or redeemed, the Rights will expire on November 17, 
2008 and will be exercisable only if a person or group becomes the beneficial 
owner of 15% or more of the Company's common stock (such person or group, a 
"15% holder") or commences a tender or exchange offer which would result in 
the offeror beneficially owning 15% or more of the Company's common stock, 
which is not approved by our Board of Directors. Each Right will entitle 
stockholders to buy one one-thousandth of a share of Series A Participating 
Preferred Stock of the Company at an exercise price of $50.00, subject to 
antidilution adjustments.

    If a person or group accumulates 15% or more of the Company's common 
stock, each Right (other than Rights held by the 15% holder) will be adjusted 
so that upon exercise the holder will have the right to receive that number 
of shares of common stock (or in some circumstances, a combination of 
securities and/or assets) having a value of twice the exercise price of the 
Right. In addition, if following a 15% acquisition the Company is involved in 
certain mergers or other business combinations, each Right (other than Rights 
held by a 15% holder) will permit each holder to purchase shares of common 
stock of the acquiring entity with a market value of twice the exercise price 
of each Right. The Board of Directors will also have the right, following a 
15% acquisition, to cause each Right (other than rights held by the 15% 
holder) to be exchanged for one share of common stock.

    The Board of Directors is entitled to redeem the Rights at $.01 per Right 
at any time prior to a 15% acquisition and in certain other specified 
situations.

(b)      Use of Proceeds

    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 underwriting of the offering was led by a group consisting of 
Morgan Stanley Dean Witter, Lehman Brothers and SBC Warburg Dillon 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 us or an affiliate of 
any 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>
<CAPTION>
      <S>                                       <C>
      Repayment of indebtedness                 $  1,279,000
      Working capital                           $ 14,836,000
      Temporary investments                     $ 22,585,000
</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 us or an 
affiliate of these persons.


                                        19
<PAGE>

(c)      Market Information

    Our common stock began trading on the National Association of Securities 
Dealers Automated Quotation ("Nasdaq") National Market on April 14, 1998, 
under the symbol "NGEN." Prior to that date, there was no established trading 
market for our common stock. The following table sets forth the range of high 
and low sales prices as reported for our common stock by Nasdaq for the 
periods indicated:

<TABLE>
<CAPTION>
                                                                High             Low
    Year Ended December 31, 1998:                               ----             ---
    -----------------------------
    <S>                                                       <C>              <C>
     2nd Quarter (from April 14, 1998)                        $ 11.250         $ 5.375
     3rd Quarter                                              $  8.375         $ 3.000
     4th Quarter                                              $  5.750         $ 2.875
</TABLE>


    As of March 5, 1999, there were approximately 262 shareholders of record of
our common stock. We have not paid any cash dividends to date and do not
anticipate any being paid in the foreseeable future.

ITEM 6.  SELECTED FINANCIAL DATA

    The selected financial data set forth below with respect to our consolidated
financial statements has been derived from the audited financial statements. The
data set forth below should be read in conjunction with "Management's Discussion
and Analysis of Financial Condition and Results of Operations" and our financial
statements and notes thereto appearing elsewhere herein:

<TABLE>
<CAPTION>
                                                                           YEARS ENDED DECEMBER 31,
                                                       ---------------------------------------------------------------
                                                           1998         1997        1996         1995        1994
                                                       -----------  -----------  -----------  -----------  --------
                                                                   (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)
<S>                                                    <C>          <C>          <C>          <C>          <C>
CONSOLIDATED STATEMENT OF OPERATIONS DATA:                                                                  
Revenues:                                                                                                   
  Sponsored research                                      $  5,461     $  1,243     $    --      $    --    $    --
  Contract and grant revenue                                 2,172        2,123       1,644          318         --
                                                          --------     --------     -------      -------    -------
     Total revenues                                          7,633        3,366       1,644          318         --
Operating expenses:                                                                                        
  Research and development                                  23,002       11,769       6,931        3,356      1,345
  General and administrative                                 6,420        3,910       2,427        1,646      1,065
  Acquired in-process technology                             1,193           --          --           --         --
                                                          --------     --------     -------      -------    -------
     Total operating expenses                               30,615       15,679       9,358        5,002      2,410
Equity in loss of joint venture                              (610)          --           --           --         --
Interest income (expense), net                               2,650          975         (64)          96         34
                                                          --------     --------     -------      -------    -------
Net loss                                                  $(20,942)    $(11,338)    $(7,778)     $(4,588)   $(2,376)
                                                          --------     --------     -------      -------    -------
                                                          --------     --------     -------      -------    -------

Net loss per share--basic and diluted                     $  (1.60)    $  (8.42)    $ (8.08)               
                                                          --------     --------     -------      
                                                          --------     --------     -------      
Number of shares used in computing net
  loss per share--basic and diluted                         13,097        1,347         963                
                                                          --------     --------     -------      
                                                          --------     --------     -------      

CONSOLIDATED BALANCE SHEET DATA:
Cash and cash equivalents                                 $ 62,245     $ 19,498    $ 16,775      $ 4,318    $   206
Working capital                                             57,701       16,775      14,853        3,931        (22)
Total assets                                                72,704       23,215      19,090        6,339      1,622
Capital lease obligations, less current portion              4,176        1,193         935          631        347
Accumulated deficit                                        (47,431)     (26,489)    (15,151)      (7,372)    (2,784)
Total stockholders' equity                                  61,051       18,599      15,680        4,950        865

</TABLE>

                                        20
<PAGE>

ITEM 7. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS

    This Form 10-K 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," 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 
previously under the caption "Factors that May Affect Results" and elsewhere 
in this Form 10-K. 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 December 31, 1998, had an accumulated 
deficit of approximately $47.4 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 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

YEARS ENDED DECEMBER 31, 1998, 1997, AND 1996

    REVENUES. For the year ended December 31, 1998, revenue from sponsored 
research totaled approximately $5.5 million compared to approximately $1.2 
million and none for the years ended December 31, 1997 and 1996, 
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 year ended December 31, 1998 was earned in 
connection with a joint venture collaboration with Becton Dickinson entered 
into in October 1997, a research and development agreement with Aventis 
Research and Technology (an affiliate of Hoechst AG), entered into in 
December 1997, and a nonexclusive research and development agreement with 
Elan entered into in December 1997. Sponsored research revenue recognized 
during the year ended December 31, 1997 was earned in connection with a 
research agreement with Becton Dickinson effective in May 1997 which was 
subsequently superceded by the joint venture collaboration entered into in 
October 1997.

    Revenue from contracts and grants totaled approximately $2.2 million for 
the year ended December 31, 1998 compared to approximately $2.1 million and 
approximately $1.6 million for the years ended December 31, 1997 and 1996, 
respectively. The increase in contract and grant revenue was due to an 
increase in the number of active contracts to seven during the year ended 
December 31, 1998 from six and three during the years ended December 31, 1997 
and 1996, respectively. During 1998, we were awarded a contract by the Space 
and Naval Warfare Systems Center San Diego for the Defense Advance Research 
Projects Agency which could total in excess of $7 million over the next five 
years. In conjunction with the acquisition of Nanotronics, Inc. in January 
1998, we assumed two contracts with the Department of the Air Force, 
Information Directorate of the Air Force Research Laboratory, Rome, New York. 
In 1997, we received funding from The National Institute of Standards and 
Technology --Advanced Technology Program under a $2.0 million two-year award 
initiated in May 1997. In 1996, we received funding from The National 
Institute of Standards and Technology -- Advanced Technology Program under a 
$2.0 million two-year award initiated in August 1995.


                                        21
<PAGE>

    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 $23.0 million during the year ended December 31, 
1998 from approximately $11.8 million and $6.9 million for the years ended 
December 31, 1997 and 1996, respectively. Research and development expenses 
include salaries, lab supplies, consulting, travel, facilities and other 
expenditures relating to research and product development. 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, development of engineering prototypes for our 
lead product, expansion of research and development facilities, and increases 
in license and research fees incurred in further exploring and developing our 
core technologies. 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 $6.4 million in 1998 compared to approximately $3.9 
million in 1997 and approximately $2.4 million in 1996. This increase is 
principally due to increased legal costs associated with enhancing and 
maintaining our intellectual property portfolio, the expansion of activities 
related to marketing our potential products, and to deferred compensation 
expense recognized during the year ended December 31, 1998 in excess of what 
was recorded during the year ended December 31, 1997. 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 expand our sales and marketing and general and 
administrative organizations and as we continue to enhance and maintain our 
intellectual property portfolio.

    ACQUIRED IN-PROCESS TECHNOLOGY. During the first quarter of 1998, we 
issued 200,000 shares of our 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 our initial public offering. The in-process technology 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 year ended December 31, 1998.

    INTEREST INCOME (EXPENSE), NET. We had net interest income of 
approximately $2.6 million in 1998 compared to net interest income of 
approximately $975,000 in 1997 and net interest expense of $64,000 in 1996. 
The significant increase in 1998 was primarily attributable 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. Proceeds from private placements between December 1996 and May 
1997 resulted in increased interest income during 1997 compared to 1996. The 
increase in interest income was partially offset by higher interest expense 
during 1998, compared to 1997 and 1996, due to greater amounts of equipment 
under capital leases in 1998 than in 1997 and 1996.

    EQUITY IN LOSS OF JOINT VENTURE. We recognized a loss of approximately 
$610,000 for the year ended December 31, 1998 from the joint venture formed 
in 1997 with Becton Dickinson, based on the loss allocation described in the 
joint venture agreement which states that losses will be allocated in 
proportion to and not to exceed cash contributions. There was no loss during 
1997 as no cash contributions were made by us to the joint venture during the 
year ended December 31, 1997.

LIQUIDITY AND CAPITAL RESOURCES

    In April 1998, we completed our initial public offering of common stock 
generating net proceeds of approximately $38.7 million. Concurrent with the 
initial public offering, we completed a private placement of our equity 
securities with Becton Dickinson, Hoechst (through a subsidiary) and Elan for 
net proceeds of $6.0 million, $10.0 million and $5.0 million, respectively. 
Prior to our initial public offering, we had financed our operations 


                                        22
<PAGE>

primarily through the net proceeds received from private placements of 
preferred equity securities totaling approximately $44.1 million.

    We fund most of our equipment acquisitions and leasehold improvements 
through capital leasing facilities. During 1998, we received proceeds from 
equipment and leasehold improvement financing of approximately $5.7 million 
compared to $1.2 million and $404,000 of proceeds received during 1997 and 
1996, respectively. 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 $15.1 million, 
$9.6 million and $6.1 million for 1998, 1997 and 1996, respectively. Cash 
used for operations was primarily related to the costs associated with the 
support of our expanding operations, including higher personnel costs, 
product development costs, license fees and legal fees relating to 
establishing and maintaining our intellectual property rights.

    At December 31, 1998, we had approximately $62.2 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 through at least the next 24 months. 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.

    In January 1998, we acquired all of the outstanding capital stock of 
Nanotronics, Inc. ("Nanotronics"). Nanotronics' research, which is currently 
funded in part through government grants with the Department of the Air 
Force, is exploratory in nature and at a very early stage. The in-process 
technology, which was acquired as a result of our purchase of Nanotronics, 
relates generally to nanotechnology and molecular electronics. Potential 
applications of the technology include high-density optical storage systems 
for electronics applications and self-assembly applications relating to 
microfabrication and nanofabrication. We anticipate that funding for 
Nanotronics will continue primarily through government grant sources until 
feasibility is demonstrated. If technological feasibility is demonstrated, we 
expect to pursue corporate partnership opportunities. Given the early stage 
of the technology, we have not yet determined which applications may be 
developed and the extent of our resources to be committed to each such 
application.

NET OPERATING LOSS CARRYFORWARDS

    As of December 31, 1998, we had federal and California net operating loss 
("NOL") carryforwards of approximately $41.4 million and $6.3 million, 
respectively, and approximately $1.7 million and $990,000 of research and 
development ("R&D") tax credits available to offset future federal and state 
income taxes, respectively. The federal and California NOL carryforwards are 
subject to alternative minimum tax limitations and to examination by the tax 
authorities. The federal tax loss carryforwards will begin expiring in 2006, 
unless previously utilized, and the California tax loss carryforwards will 
continue to expire in 1999, unless previously utilized. The federal and 
California R&D tax credit carryforwards will begin expiring in 2007 unless 
previously utilized. We believe that our initial public offering combined 
with the concurrent private placement, which occurred in April 1998, may 
constitute a "change of ownership" under federal income tax regulations. As 
such, we may be limited in the amount of NOLs incurred prior to our initial 
public offering, which may be utilized to offset future taxable 


                                        23
<PAGE>

income. Similar limitations may also apply to utilization of R&D tax credits 
to offset taxes payable. However, we do not believe such limitations will 
have a material impact on our ability to utilize the NOLs. See Note 9 of 
Notes to Financial Statements.

YEAR 2000 COMPLIANCE

    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.

    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 developed a reasonably likely worst case scenario with 
respect to Year 2000 problems we may encounter.

ITEM 7A.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

    None.

ITEM 8.  FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

    Refer to the Index on Page F-1 of the Financial Report included herein.

ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND 
FINANCIAL DISCLOSURE

    None.


                                        24
<PAGE>

                                    PART III

ITEM 10.  DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

    Information regarding Directors is incorporated by reference to the 
section entitled "Election of Directors" in the Nanogen, Inc. definitive 
Proxy Statement to be filed with the Securities and Exchange Commission in 
connection with the Annual Meeting of Stockholders to be held on June 30, 
1999 (the "Proxy Statement"). Information regarding Executive Officers is 
incorporated by reference to the Proxy Statement under the heading "Executive 
Officers of the Registrant." Information regarding Section 16 reporting 
compliance is incorporated by reference to the Proxy Statement under the 
heading "Section 16 Beneficial Ownership Reporting Compliance." 

ITEM 11.  EXECUTIVE COMPENSATION

    The information required by this item is incorporated by reference to the 
Proxy Statement under the heading "Executive Compensation."

ITEM 12.  SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

    The information required by this item is incorporated by reference to the 
Proxy Statement under the heading "Security Ownership of Certain Beneficial 
Owners and Management."

ITEM 13.  CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

    The information required by this item is incorporated by reference to the 
Proxy Statement under the heading "Certain Transactions."

                                     PART IV

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

    (a)(1)        Financial Statements:

    Our financial statements are included herein as required under Item 8 of 
this Annual Report on Form 10-K. See Index on page F-1.

      (2) Financial Statement Schedules

          Financial statement schedules have been omitted since they are 
either not required, not applicable, or the information is otherwise included.

      (3) Exhibits

<TABLE>
<CAPTION>
          Exhibit
          Number           Description of Document
          -------          -----------------------
          <S>              <C>
          2.1*             Agreement and Plan of Merger among the Registrant,
                           Nanotronics, Inc. ("Nanotronics") and the
                           shareholders of Nanotronics, dated as of December 18,
                           1997.
          3.(i)1           Restated Certificate of Incorporation.
          3.(i)2           Certificate of Designation, as filed with the
                           Delaware Secretary of State on November 23, 1998.
          3.(ii)*          Amended and Restated Bylaws of the Registrant.
                           (3.(ii)2)
          4.1*             Form of Common Stock Certificate.
          10.1*(A)         1997 Stock Incentive Plan of Nanogen, Inc. ("1997
                           Plan"). (10.3)
          10.2*(A)         Form of Incentive Stock Option Agreement under the
                           1997 Plan. (10.4)
          10.3*(A)         Form of Nonqualified Stock Option Agreement under the
                           1997 Plan. (10.5)
          10.4*(A)         Nanogen, Inc. Employee Stock Purchase Plan. (10.6)


                                        25
<PAGE>

          10.5*(A)         Form of Indemnification Agreement between the
                           Registrant and its directors and executive officers.
                           (10.7)
          10.6*(+)         Agreement between the Registrant and Elan
                           Corporation, plc, dated December 19, 1997. (10.8)
          10.7*(+)         Agreement between the Registrant and Hoechst AG,
                           dated December 4, 1997. (10.9)
          10.8*(+)         Agreement between the Registrant and Syntro
                           Corporation, dated of November 24, 1997. (10.10)
          10.9*(+)         Master Agreement between the Registrant and Becton,
                           Dickinson and Company, dated as of October 1, 1997,
                           with related attachments. (10.11)
          10.10*(+)        Exclusive Option Agreement between the Registrant and
                           Billups-Rothenberg, Inc., dated as of September 12,
                           1997. (10.12)
          10.11*(+)        Sponsored Research Agreement between the Registrant
                           and Prolinx, Inc., dated as of December 18, 1996.
                           (10.13)
          10.12*(+)        Collaborative Research Agreement between the
                           Registrant and the University of Texas Southwestern
                           Medical Center at Dallas, dated as of August 1, 1995.
                           (10.14)
          10.13*(+)        License Agreement between the Registrant and The Salk
                           Institute for Biological Studies, dated as of April
                           1, 1993. (10.15)
          10.14*           Form of Series B Preferred Stock Purchase Warrant,
                           between the Registrant and certain purchasers of its
                           Series B Preferred Stock, dated April 11, 1995.
                           (10.17)
          10.15*           Amended and Restated Investors' Rights Agreement
                           between the Registrant and certain securityholders
                           set forth therein, dated as of May 5, 1997, as
                           amended. (10.18)
          10.16*           Master Lease Agreement between the Registrant and
                           Mellon US Leasing, dated September 11, 1997. (10.19)
          10.17*           Lease Agreement between the Registrant and LMP
                           Properties, Ltd., dated June 29, 1994. (10.20)
          10.18*           Lease Agreement between the Registrant and Lease
                           Management Services, Inc., dated April 26, 1994, as
                           amended on December 13, 1994 and June 13, 1996.
                           (10.21)
          10.19*(A)        Form of Nanogen, Inc. Restricted Stock Issuance
                           Agreement between the Registrant and certain of its
                           directors and executive officers, dated as of
                           November 7, 1997. (10.22)
          10.20*(A)        Form of Promissory Note between the Registrant and
                           certain of its executive officers, dated August 22,
                           1996. (10.23)
          10.21*(A)        Form of Promissory Note between the Registrant and
                           certain of its executive officers, dated June 30,
                           1995. (10.24)
          10.22*(A)        Form of Common Stock Purchase Agreement. (10.25)
          10.23*(A)        Form of Performance Stock Option Agreement. (10.26)
          10.24*(A)        Agreement between the Registrant and Tina S. Nova,
                           Ph.D., dated January 5, 1994. (10.27)
          10.25*(A)        Agreement between the Registrant and W. J. Kitchen,
                           dated October 28, 1997. (10.28)
          10.26*(A)        Agreement between the Registrant and James P.
                           O'Connell, Ph.D., dated November 15, 1994. (10.29)
          10.27*(A)        Agreement between the Registrant and Harry J.
                           Leonhardt, dated May 24, 1996. (10.30)
          10.28*(A)        Agreement between the Registrant and Kieran T.
                           Gallahue, dated December 18, 1997. (10.31)
          10.29*(A)        Secured Promissory Note and Deed of Trust, between
                           the Registrant and W. J. Kitchen, dated March 16,
                           1998. (10.32)
          10.30*           Series D. Preferred Stock Purchase Warrant between
                           the Registrant and Dominion Fund II, dated January
                           26, 1998. (10.33)
          10.31*(+)        License Agreement between the Registrant and
                           Billups-Rothenberg, Inc., dated as of March 18, 1998.
                           (10.34)


                                        26
<PAGE>

          10.32***         Rights Agreement dated as of November 17, 1998,
                           between the Company and BankBoston, N.A.
          10.33**(A)       Agreement between the Registrant and Daniel D.
                           Burgess, dated July 6, 1998. (10.35)
          10.34(++)        Collaborative Research and Development Agreement
                           between the Company and Hoechst Research and
                           Technology, dated December 3, 1998.
          23.1             Consent of Ernst & Young LLP, independent auditors.
          27.1             Financial Data Schedule.
</TABLE>

      *   Incorporated by reference to the Company's Registration Statement on
          Form S-1 (File No. 333-42791). Parenthetical references following the
          description of each document relate to the exhibit number under which
          such exhibit was initially filed.
      **  Incorporated by reference to Exhibit 10.35 of the Company's Quarterly
          Report on Form 10-Q for the quarter ended September 30, 1998.
      *** Incorporated by reference to Exhibit 4.1 of the Company's Registration
          Statement on Form 8-A, filed on November 24, 1998.
      (A) Indicates management compensatory plan on arrangement.
      (+) Confidential treatment has been granted for certain portions of these
          agreements.
      (++)Confidential treatment has been requested for certain portions of this
          agreement.

    (b)   Reports on Form 8-K

          On November 24, 1998, we filed a report on Form 8-K to disclose the
Shareholder Rights Plan approved by the Board of Directors on November 17, 1998.


                                        27
<PAGE>

                                   SIGNATURES


    Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the registrant has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized.

                                             NANOGEN, INC.


Date:  March 24, 1999                        By:/s/   HOWARD C. BIRNDORF
                                                -------------------------------
                                                Howard C. Birndorf
                                                Chairman of the Board and
                                                Chief Executive Officer

    Pursuant to the requirements to the Securities Exchange Act of 1934, this
report has been signed below by the following persons on behalf of the
registrant and in the capacities and on the dates indicated.

<TABLE>
<CAPTION>

Signature                                      Title                                    Date
---------                                      -----                                    ----
<S>                                            <C>                                      <C>
/s/  HOWARD C. BIRNDORF                        Chairman of the Board and                March 24, 1999
------------------------------------           Chief Executive Officer       
          Howard C. Birndorf                   (Principal Executive Officer) 

                                               
/s/    TINA S. NOVA, PH.D.                     Director, President and                  March 24, 1999
------------------------------------           Chief Operating Officer
           Tina S. Nova, Ph.D.                 


/s/    DANIEL D. BURGESS                       Vice President, Chief Financial          March 24, 1999
------------------------------------           Officer (Principal Financial and 
             Daniel D. Burgess                 Accounting Officer)              
                                               
/s/        BROOK H. BYERS                      Director                                 March 24, 1999
------------------------------------
               Brook H. Byers


/s/        CAM L. GARNER                       Director                                 March 24, 1999
------------------------------------
               Cam L. Garner


/s/   DAVID G. LUDVIGSON                       Director                                 March 24, 1999
------------------------------------
          David G. Ludvigson


/s/     THOMAS G. LYNCH                        Director                                 March 24, 1999
------------------------------------
            Thomas G. Lynch
</TABLE>

                                        28
<PAGE>

                                  NANOGEN, INC.
                   INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

<TABLE>
<CAPTION>
                                                                          Page
                                                                          ----
<S>                                                                       <C>
Report of Ernst & Young LLP, Independent Auditors....................      F-2

Consolidated Balance Sheets..........................................      F-3

Consolidated Statements of Operations................................      F-4

Consolidated Statements of Cash Flows................................      F-5

Consolidated Statements of Stockholders' Equity......................      F-6

Notes to Consolidated Financial Statements........................... F-7-F-15
</TABLE>





                                       F-1
<PAGE>



                REPORT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS


The Board of Directors and Stockholders
Nanogen, Inc.

We have audited the accompanying consolidated balance sheets of Nanogen, Inc.,
as of December 31, 1998 and 1997, and the related consolidated statements of
operations, stockholders' equity, and cash flows for each of the three years in
the period ended December 31, 1998. These financial statements are the
responsibility of the Company's management. Our responsibility is to express an
opinion on these financial statements based on our audits.

We conducted our audits in accordance with generally accepted auditing
standards. Those standards require that we plan and perform the audit to obtain
reasonable assurance about whether the financial statements are free of material
misstatement. An audit includes examining, on a test basis, evidence supporting
the amounts and disclosures in the financial statements. An audit also includes
assessing the accounting principles used and significant estimates made by
management, as well as evaluating the overall financial statement presentation.
We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the financial statements referred to above present fairly, in
all material respects, the consolidated financial position of Nanogen, Inc. at
December 31, 1998 and 1997 and the consolidated results of its operations and
its cash flows for each of the three years in the period ended December 31,
1998, in conformity with generally accepted accounting principles.



                                       ERNST & YOUNG LLP




San Diego, California
January 22, 1999


                                       F-2
<PAGE>

                                  NANOGEN, INC.

                           CONSOLIDATED BALANCE SHEETS
                        (IN THOUSANDS, EXCEPT SHARE DATA)

<TABLE>
<CAPTION>
                                                                      DECEMBER 31,
                                                                 ---------------------
                                                                    1998        1997
                                                                 ---------   ---------
<S>                                                              <C>         <C>
                            ASSETS
Current assets:                                                               
  Cash and cash equivalents                                      $  62,245   $  19,498
  Receivables and other current assets                               2,933         700
                                                                 ---------   ---------
    Total current assets                                            65,178      20,198

Property and equipment, net                                          6,980       2,440
Restricted cash                                                        270         359
Other assets                                                           276         218
                                                                 ---------   ---------
                                                                 $  72,704   $  23,215
                                                                 ---------   ---------
                                                                 ---------   ---------


             LIABILITIES AND STOCKHOLDERS' EQUITY                             

Current liabilities:                                                          
  Accounts payable                                               $   1,066   $     597
  Accrued liabilities                                                1,433       1,009
  Deferred revenue                                                   3,065       1,012
  Current portion of capital lease obligations                       1,913         805
                                                                 ---------   ---------
    Total current liabilities                                        7,477       3,423

Capital lease obligations, less current portion                      4,176       1,193

Commitments                                                             --          --

Stockholders' equity:                                                         
  Convertible preferred stock, $.001 par value, 5,000,000 and
    15,500,000 shares authorized at December 31, 1998 and 1997,
    respectively; no shares and 13,683,865
    shares issued and outstanding at December 31,                       --          14
    1998 and 1997, respectively
  Common stock, $.001 par value, 50,000,000 and 40,000,000 shares
    authorized at December 31, 1998 and 1997, respectively;
    18,835,461 and 3,183,523 shares
    issued and outstanding at December 31, 1998 and                     19           3
    1997, respectively
  Additional paid-in capital                                       111,489      48,523
  Deferred compensation                                             (1,512)     (2,323)
  Notes receivable from officers                                    (1,514)     (1,129)
  Accumulated deficit                                              (47,431)    (26,489)
                                                                 ---------   ---------
Total stockholders' equity                                          61,051      18,599
                                                                 ---------   ---------
                                                                 $  72,704   $  23,215
                                                                 ---------   ---------
                                                                 ---------   ---------
</TABLE>
                             See accompanying notes.





                                       F-3

<PAGE>

                                  NANOGEN, INC.

                      CONSOLIDATED STATEMENTS OF OPERATIONS
                      (IN THOUSANDS, EXCEPT PER SHARE DATA)

<TABLE>
<CAPTION>
                                                      YEARS ENDED DECEMBER 31,
                                                -----------------------------------
                                                   1998         1997         1996
                                                ---------    ---------     --------
<S>                                             <C>          <C>           <C>
Revenues:                                                                  
  Sponsored research                            $   5,461    $   1,243     $     --
  Contract and grant revenue                        2,172        2,123        1,644
                                                ---------    ---------     --------
Total revenues                                      7,633        3,366        1,644

Operating expenses:                                                        
  Research and development                         23,002       11,769        6,931
  General and administrative                        6,420        3,910        2,427
  Acquired in-process technology                    1,193           --           --
                                                ---------    ---------     --------
Total operating expenses                           30,615       15,679        9,358
                                                ---------    ---------     --------

Loss from operations                              (22,982)     (12,313)      (7,714)

Equity in loss of joint venture                      (610)          --           --
Interest income (expense), net                      2,650          975          (64)
                                                ---------    ---------     ---------
Net loss                                        $ (20,942)   $ (11,338)    $ (7,778)
                                                ---------    ---------     ---------
                                                ---------    ---------     ---------

Net loss per share-- basic and diluted          $   (1.60)   $   (8.42)    $   (8.08)
                                                ---------    ---------     ---------
                                                ---------    ---------     ---------
Number of shares used in computing net loss
  per share-- basic and diluted                    13,097        1,347           963
                                                ---------    ---------     ---------
                                                ---------    ---------     ---------
</TABLE>
                             See accompanying notes.





                                       F-4
<PAGE>

                                  NANOGEN, INC.

                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)

<TABLE>
<CAPTION>
                                                                    YEARS ENDED DECEMBER 31,
                                                              -----------------------------------
                                                                1998         1997          1996
                                                              --------     --------      --------
<S>                                                           <C>          <C>           <C>
OPERATING ACTIVITIES:                                                                   
  Net loss                                                    $(20,942)    $(11,338)     $ (7,778)
  Adjustments to reconcile net loss to net cash used in                                 
  operating activities:
    Acquisition of in-process technology                         1,193           --            --
    Equity in loss of joint venture                                610           --            --
    Net (gain)/loss from sale of property, plant &                 (13)          --            --
    equipment
    Depreciation and amortization                                1,168          527           351
    Interest expense converted into convertible                     --           --            20
    preferred stock
    Amortization of deferred compensation                        2,181          611            --
    Changes in operating assets and liabilities:                                        
      Accounts payable                                             469          117           276
      Accrued liabilities                                          424         (414)        1,175
      Deferred revenue                                           2,053        1,012            --
      Receivables and other current assets                      (2,233)        (145)         (182)
                                                              --------     --------      --------
Net cash used in operating activities                          (15,090)      (9,630)       (6,138)

INVESTING ACTIVITIES:                                                                   
  Purchase of equipment                                            (72)        (492)         (114)
  Proceeds from sale of assets                                      29           --            --
  Investment in joint venture                                     (610)          --            --
                                                              --------     --------      --------
Net cash used in investing activities                             (653)        (492)         (114)

CASH FLOWS FROM FINANCING ACTIVITIES:                                                   
  Restricted cash                                                   89           50            56
  Principal payments on capital lease obligations               (1,561)        (670)         (427)
  Proceeds from capital lease financing                             --           --           593
  Issuance of notes payable to stockholders                         --           --         2,000
  Issuance of common stock                                      60,052          125            41
  Issuance of convertible preferred stock, net of                   43       13,525        16,448
  issuance costs
  Interest on notes receivable from officers                       (75)          (4)           (2)
  Other assets                                                     (58)        (181)           --
                                                              --------     --------      --------
Net cash provided by financing activities                       58,490       12,845        18,709
                                                              --------     --------      --------
Increase in cash and cash equivalents                           42,747        2,723        12,457
Cash and cash equivalents at beginning of year                  19,498       16,775         4,318
                                                              --------     --------      --------
Cash and cash equivalents at end of year                      $ 62,245     $ 19,498      $ 16,775
                                                              --------     --------      --------
                                                              --------     --------      --------

SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION:                                       
Interest paid                                                 $    466     $    225      $    188
                                                              --------     --------      --------
                                                              --------     --------      --------
SUPPLEMENTAL SCHEDULE OF NONCASH INVESTING AND FINANCING                                
ACTIVITIES:
Equipment acquired under capital leases                       $  5,652     $  1,159      $    404
                                                              --------     --------      --------
                                                              --------     --------      --------
Issuance of convertible preferred stock in exchange for
  cancellation of debt and related accrued interest           $     --     $     --      $  2,021
                                                              --------     --------      --------
                                                              --------     --------      --------
Common stock issued in exchange for notes receivables
  from officers                                               $    310     $  1,057      $     --
                                                              --------     --------      --------
                                                              --------     --------      --------
Issuance of convertible preferred stock and warrants in
  exchange for in-process technology                          $  1,193     $     --      $     --
                                                              --------     --------      --------
                                                              --------     --------      --------

Deferred compensation related to stock options                $  1,370     $  2,934      $     --
                                                              --------     --------      --------
                                                              --------     --------      --------
</TABLE>



                             See accompanying notes.




                                       F-5
<PAGE>

                                  NANOGEN, INC.

                 CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY
                                 (IN THOUSANDS)

<TABLE>
<CAPTION>
                                                     CONVERTIBLE                                       
                                                   PREFERRED STOCK        COMMON STOCK       ADDITIONAL
                                                  -----------------    ------------------     PAID-IN  
                                                  SHARES     AMOUNT    SHARES      AMOUNT     CAPITAL  
                                                  -------    ------    -------     ------    ----------
<S>                                               <C>        <C>       <C>         <C>       <C>
Balance at December 31, 1995                        5,814     $   6      1,331       $  1    $  12,347 
  Issuance of common stock                             --        --        284          1           42 
  Repurchase of common stock                           --        --        (16)        --           (2)
  Issuance of convertible preferred stock           4,971         5         --         --       18,464 
  Exercise of stock option in exchange for
    notes receivable and accrued interest              --        --        233         --           35 
  Net loss                                             --        --         --         --           -- 
                                                  -------     -----     ------       ----    --------- 
Balance at December 31, 1996                       10,785        11      1,832          2       30,886 
  Issuance of common stock                             --        --        207         --          129 
  Repurchase of common stock                           --        --        (30)        --           (4)
  Issuance of convertible preferred stock           2,899         3         --         --       13,522 
  Deferred compensation related to stock               --        --         --         --        2,934 
  options
  Amortization of deferred compensation                --        --         --         --           -- 
  Exercise of stock options in exchange for
    notes receivable and accrued interest              --        --      1,175          1        1,056 
  Net loss                                             --        --         --         --           -- 
                                                  -------     -----     ------       ----    --------- 
Balance at December 31, 1997                       13,684        14      3,184          3       48,523 
  Repurchase of common stock                           --        --       (123)        --         (103)
  Exercise of stock options                            --        --        115         --           91 
  Sale of stock under employee stock purchase          --        --         27         --          108 
  plan
  Issuance of common stock pursuant to                                                                 
  exercise
    of warrants                                        --        --        413          1          130 
  Issuance of convertible preferred stock             232        --         --         --        1,236 
  Sale of common stock under initial public                                                            
    offering, net of expenses                          --        --      3,900          4       38,731 
  Sale of common stock in private placement in                                                         
    conjunction with initial public offering           --        --      1,909          2       20,998 
  Conversion of preferred stock upon the                                                               
    the completion of initial public offering     (13,916)      (14)     9,277          9            5 
  Deferred compensation related to stock               --        --         --         --        1,370 
  options
  Amortization of deferred compensation                --        --         --         --           -- 
  Exercise of stock options in exchange for                                                            
    notes receivable and accrued interest              --        --        133         --          400 
  Net loss                                             --        --         --         --           -- 
                                                  -------     -----     ------       ----    --------- 
Balance at December 31, 1998                           --     $  --     18,835       $ 19    $ 111,489 
                                                  =======     =====     ======       ====    ========= 
</TABLE>

<TABLE>
<CAPTION>
                                                                      NOTES                        TOTAL     
                                                                    RECEIVABLE                 STOCKHOLDERS'
                                                    DEFERRED           FROM       ACCUMULATED     EQUITY    
                                                  COMPENSATION       OFFICERS       DEFICIT     (DEFICIT)  
                                                  ------------      ----------   ------------  ------------
<S>                                               <C>              <C>           <C>           <C>
Balance at December 31, 1995                       $     --        $   (31)       $ (7,373)      $  4,950 
  Issuance of common stock                               --             --              --             43 
  Repurchase of common stock                             --             --              --             (2)
  Issuance of convertible preferred stock                --             --              --         18,469 
  Exercise of stock option in exchange for                                                                
    notes receivable and accrued interest                --            (37)             --             (2)
  Net loss                                               --             --          (7,778)        (7,778)
                                                    -------        -------        --------       -------- 
Balance at December 31, 1996                             --            (68)        (15,151)        15,680 
  Issuance of common stock                               --             --              --            129 
  Repurchase of common stock                             --             --              --             (4)
  Issuance of convertible preferred stock                --             --              --         13,525 
  Deferred compensation related to stock             (2,934)            --              --             -- 
  options                                                                                                 
  Amortization of deferred compensation                 611             --              --            611 
  Exercise of stock options in exchange for                                                               
    notes receivable and accrued interest                --         (1,061)             --             (4)
  Net loss                                               --             --         (11,338)       (11,338)
                                                    -------        -------        --------       -------- 
Balance at December 31, 1997                         (2,323)        (1,129)        (26,489)        18,599 
  Repurchase of common stock                             --             90              --            (13)
  Exercise of stock options                              --             --              --             91 
  Sale of stock under employee stock purchase            --             --              --            108 
  plan                                                                                                    
  Issuance of common stock pursuant to                                                                    
  exercise                                                                                                
    of warrants                                          --             --              --            131 
  Issuance of convertible preferred stock                --             --              --          1,236 
  Sale of common stock under initial public                                                               
    offering, net of expenses                            --             --              --         38,735 
  Sale of common stock in private placement in                                                            
    conjunction with initial public offering             --             --              --         21,000 
  Conversion of preferred stock upon the                                                                  
    the completion of initial public offering            --             --              --             -- 
  Deferred compensation related to stock             (1,370)            --              --             -- 
  options                                                                                                 
  Amortization of deferred compensation               2,181             --              --          2,181 
  Exercise of stock options in exchange for                                                               
    notes receivable and accrued interest                --           (475)             --            (75)
  Net loss                                               --             --         (20,942)       (20,942)
                                                    -------        -------        --------       -------- 
Balance at December 31, 1998                        $(1,512)       $(1,514)       $(47,431)      $ 61,051 
                                                    -------        -------        --------       -------- 
                                                    -------        -------        --------       -------- 
</TABLE>

                             See accompanying notes.



                                       F-6

<PAGE>

                                  NANOGEN, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS


1.  ORGANIZATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

    ORGANIZATION AND BUSINESS ACTIVITY

    Nanogen, Inc. ("Nanogen" or the "Company") was incorporated in California on
November 6, 1991 as Nanophore, Inc. ("Nanophore"), a wholly-owned subsidiary of
Nanotronics, Inc. ("Nanotronics"), and pursuant to a Plan of Corporate
Separation and Reorganization, Nanophore issued shares of its common stock to
the Nanotronics shareholders and commenced operations as Nanogen, Inc. on
September 1, 1993. In November 1997, the Company reincorporated in Delaware. The
Company was established to develop products in the area of medical diagnostics,
biomedical research, genomics, genetic testing and drug discovery by combining
advanced microelectronics with molecular biology.

    ACQUISITION OF NANOTRONICS, INC.

    In January 1998, the Company consummated an Agreement and Plan of Merger
with Nanotronics, Inc. ("Nanotronics"), pursuant to which a wholly owned
California subsidiary of the Company merged with and into Nanotronics. Upon the
consummation of the merger, the Company issued approximately 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. This Series D Preferred Stock
converted into 132,334 shares of common stock at the Company's initial public
offering. The transaction has been accounted for using the purchase method. The
operations and net assets of Nanotronics are not material to the Company's
financial position or results of operations, but have been consolidated in the
Company's financial statements since the date of acquisition. The technological
feasibility of the acquired technology has not been established nor have
alternative uses been identified, therefore, the purchase price of approximately
$1.2 million has been allocated to acquired in-process technology and has been
reflected as a charge in the Company's statement of operations.

    The following unaudited table shows the pro forma amounts as if the
acquisition had occurred on January 1, 1997:

<TABLE>
<CAPTION>
                                                            YEARS ENDED DECEMBER 31,
                                                       --------------------------------
                                                              1998           1997
                                                        -------------    -------------    
                   <S>                                  <C>              <C>
                   Revenue                                 $    7,667      $    3,699
                   Net loss                                $  (19,753)     $  (12,667)
                   Net loss per share - basic and          $    (1.51)     $    (9.40)
                   diluted
</TABLE>

    CASH AND CASH EQUIVALENTS

    Cash and cash equivalents consist of cash and highly liquid investments
which include debt securities with remaining maturities of three months or less
when acquired.

    CONCENTRATION OF CREDIT RISK

    Cash and cash equivalents are financial instruments, which potentially
subject the Company to concentration of credit 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. The Company has established guidelines relative to diversification and
maturities to maintain safety and liquidity. These guidelines are reviewed
periodically and modified to take advantage of trends in yields and interest
rates. The Company has not experienced any material losses on its investments.

    All of the Company's investments are with financial institutions and
organizations with strong credit ratings with maturities of ninety days or less
when acquired.


                                       F-7
<PAGE>

    RESTRICTED CASH

    During 1994, the Company obtained an irrevocable standby letter of credit 
in the amount of $463,775 to secure its building lease. The letter of credit 
is secured by a certificate of deposit, which is shown as restricted cash in 
the accompanying balance sheet. The letter of credit is reduced by 
approximately $50,000 annually, and had a balance of approximately $263,775 
at December 31, 1998.

    PROPERTY AND EQUIPMENT

    Property and equipment is stated at cost and depreciated over the 
estimated useful lives of the assets (5 years) using the straight-line 
method. Leasehold improvements are stated at cost and amortized on a 
straight-line basis over the shorter of the estimated useful lives of the 
assets or the lease term.

    REVENUE RECOGNITION

    Contract, grant and sponsored research revenue are recorded as the costs 
and expenses to perform the research are incurred. Payments received in 
advance under these arrangements are recorded as deferred revenue until the 
expenses are incurred. Continuation of certain contracts, grants, and 
research agreements are dependent upon the company achieving specific 
contractual milestones.

    Contract and grant revenue from one customer amounted to approximately 
10%, 45% and 70% of total revenues in 1998, 1997 and 1996, respectively. 
Contract and grant revenue from a second customer amounted to 7%, 13% and 23% 
in 1998, 1997 and 1996, respectively. Additionally, sponsored research (see 
Note 10) was 72% and 37% of total revenue in 1998 and 1997, respectively.

    NEW ACCOUNTING STANDARDS

    In June 1997, the Financial Accounting Standards Board issued SFAS No. 
130, REPORTING COMPREHENSIVE INCOME, and SFAS No. 131, SEGMENT INFORMATION. 
Both of these standards are effective for fiscal years beginning after 
December 15, 1997. SFAS No. 130 requires that all components of comprehensive 
income, including net income, be reported in the financial statements in the 
period in which they are recognized. Comprehensive income is defined as the 
change in equity during a period from transactions and other events and 
circumstances from non-owner sources. Net income and other comprehensive 
income, including foreign currency translation adjustments, and unrealized 
gains and losses on investments, shall be reported, net of their related tax 
effect, to arrive at comprehensive income. Comprehensive loss was not 
different than net loss. SFAS No. 131 amends the requirements for public 
enterprises to report financial and descriptive information about its 
reportable operating segments. Operating segments, as defined in SFAS No. 
131, are components of an enterprise for which separate financial information 
is available and is evaluated regularly by the Company in deciding how to 
allocate resources and in assessing performance. The financial information is 
required to be reported on the basis that is used internally for evaluating 
the segment performance. The Company operates in one business and operating 
segment and the adoption of SFAS No. 131 did not have an impact on the 
Company's financial statements.

    NET LOSS PER SHARE

    Basic net loss per share has been computed using the weighted average 
number of common shares outstanding during the periods presented. Common 
equivalent shares resulting from outstanding preferred stock, options to 
purchase common stock and warrants to purchase convertible preferred stock 
are excluded from the computation of diluted net loss per share as their 
effect is antidilutive.

    Recent interpretations by the Securities and Exchange Commission have 
altered the treatment of preferred stock previously included in computing 
certain earnings-per-share data. The Company previously considered 
convertible preferred stock as outstanding in pre-IPO periods from the date 
of the original issuance in computing earnings per share. To conform with the 
recent interpretations, the Company has revised its calculation of earnings 
per share for all pre-IPO periods to exclude the impact of convertible 
preferred shares.


                                       F-8
<PAGE>

    STOCK-BASED COMPENSATION

    As permitted by Statement of Financial Accounting Standards No. 123, the 
Company has elected to follow Accounting Principles Board Opinion No. 25, 
ACCOUNTING FOR STOCK ISSUED TO EMPLOYEES, and related Interpretations ("APB 
25"), in accounting for its employee stock options. Under APB 25, when the 
exercise price of the Company's employee stock options is not less than the 
fair value of the underlying stock on the date of grant, no compensation 
expense is recognized.

    USE OF ESTIMATES

    The preparation of financial statements in conformity with generally 
accepted accounting principles requires management to make estimates and 
assumptions that affect the reported amounts of assets and liabilities and 
related disclosures at the date of the financial statements, and the amounts 
of revenues and expenses reported during the period. Actual results could 
differ from those estimates.

    STOCKHOLDERS' EQUITY

    In November 1997, the Company reincorporated in Delaware and established 
$.001 par value common and preferred stock. The accompanying financial 
statements have been retroactively reclassified to reflect the effects of the 
reincorporation.

    INITIAL PUBLIC OFFERING

    In April 1998, the Company completed an initial public offering (the 
"offering") of 3,900,000 shares of common stock, providing the Company with 
net proceeds of approximately $38.7 million. All outstanding shares of 
convertible preferred stock outstanding at April 13, 1998 automatically 
converted into 9,277,275 common shares upon the closing of the offering. 
Prior to the closing of the offering, the Company effected a 2-for-3 reverse 
stock split. All common stock share numbers have been retroactively adjusted 
to reflect this 2-for-3 stock split.

    Concurrently with the offering, the Company completed a private placement 
of 1,909,089 shares of its common stock to Becton, Dickinson and Company, 
Hoechst AG (through a subsidiary) and Elan Corporation, plc, resulting in net 
proceeds to the Company of $6.0 million, $10.0 million and $5.0 million, 
respectively.

2.  PROPERTY AND EQUIPMENT

    Property and equipment consist of the following (in thousands):

<TABLE>
<CAPTION>
                                                                                DECEMBER 31,
                                                                          -------------------------
                                                                             1998          1997
                                                                          ----------    -----------
                   <S>                                                    <C>           <C>
                   Scientific equipment                                   $    3,130    $     2,059
                   Office furniture and equipment                              2,030            946
                   Leasehold improvements                                      4,141            646
                                                                          ----------    -----------
                                                                               9,301          3,651
                   Less accumulated depreciation and amortization             (2,321)        (1,211)
                                                                          ----------    -----------
                                                                          $    6,980    $     2,440
                                                                          ----------    -----------
                                                                          ----------    -----------
</TABLE>

3.  ACCRUED LIABILITIES

    Accrued liabilities are comprised of the following (in thousands):

<TABLE>
<CAPTION>
                                                                                DECEMBER 31,
                                                                          -------------------------
                                                                             1998          1997
                                                                          ----------    -----------
                   <S>                                                    <C>           <C>
                   Accrued compensation                                   $      754    $       608
                   Other                                                         679            401
                                                                          ----------    -----------
                                                                          $    1,433    $     1,009
                                                                          ----------    -----------
                                                                          ----------    -----------
</TABLE>



                                       F-9

<PAGE>

4.  COMMITMENTS

    LICENSING AND RESEARCH AGREEMENTS

    The Company is a party to licensing and research agreements with various
entities whereby the Company is obligated to pay certain license fees and
research funding. None of these agreements individually are considered material.
Under some of these agreements, the Company may be required to pay royalties on
future sales in the event that the Company incorporates the licensed technology
in one or more of its potential commercial products.

    LEASES

    The Company leases its facilities and certain equipment under operating
lease agreements that expire at various dates through 2005. The minimum annual
rents are subject to specified annual rental increases. Rent expense was
approximately $532,000, $461,000 and $443,000 in 1998, 1997, and 1996,
respectively.

    The Company leases certain equipment under capital lease obligations. Cost
and accumulated amortization of equipment under capital lease were approximately
$9,045,000 and $2,199,000 at December 31, 1998 and $3,365,000 and $1,142,000 at
December 31, 1997, respectively.

    Annual future minimum obligations for operating and capital leases as of
December 31, 1998 are as follows (in thousands):

<TABLE>
<CAPTION>
                                                                                       CAPITAL
                                                                          OPERATING     LEASE
                                                                           LEASES     OBLIGATIONS
                                                                         ----------  ------------
          <S>                                                            <C>         <C>
          1999                                                           $      599  $    2,506
          2000                                                                  612       2,284
          2001                                                                  626       1,837
          2002                                                                  651         419
          2003                                                                  677          --
          Thereafter                                                            882          --
                                                                         ----------  ----------
          Total minimum lease payments                                   $    4,047       7,046
                                                                         ----------
                                                                         ----------
          Less amount representing interest                                                 957
                                                                                     ----------
          Present value of future minimum capital lease obligations                       6,089
          Less amounts due in one year                                                    1,913
                                                                                     ----------
          Long term portion of capital lease obligations                             $    4,176
                                                                                     ----------
                                                                                     ----------
</TABLE>

    As of December 31, 1998, the Company has approximately $1.4 million of
available funding under equipment lease lines.

5.  RELATED PARTY TRANSACTIONS

    In November 1998 the Company entered into a Standstill Agreement and Right
of First Negotiation (the "Agreement") with Graviton, Inc. ("Graviton"),
granting the Company an exclusive period of time to negotiate a license to
certain technologies licensed to and/or developed by Graviton. In exchange for
the Agreement, the Company advanced to Graviton through a secured loan the sum
of $500,000. If a license agreement is negotiated, the $500,000 loan will be
creditable against any license fees due thereunder. Messrs. Birndorf and Byers,
both directors of the Company, are also directors of and investors in Graviton.
Additionally, Dr. Tina Nova, the Company's President and Chief Operating
Officer, is the spouse of the president of Graviton, Dr. Michael Nova. Together,
Messrs. Birndorf, Byers and Nova hold a controlling ownership interest in
Graviton. Given the interrelationship among the parties, the Company's Board
appointed a committee of disinterested Board members to evaluate this
opportunity. After full disclosure of the above-referenced interrelationships,
the Committee determined that it was in the best interests of the Company to
proceed as outlined.


                                       F-10
<PAGE>

6.  STOCKHOLDERS' EQUITY

    CONVERTIBLE PREFERRED STOCK

    In December 1997, the Board of Directors authorized, following the 
offering, 5,000,000 shares of undesignated preferred stock at a par value of 
$.001. The Board of Directors has the authority, without further action by 
the stockholders, to issue from time to time the preferred stock in one or 
more series and to fix the number of shares, designations, preferences, 
powers, and relative, participating, optional or other special rights and the 
qualifications or restrictions thereof. At December 31, 1998, there was no 
preferred stock outstanding.

    WARRANTS

    At December 31, 1998, there were outstanding warrants to purchase an 
aggregate of 26,084 shares of common stock at exercise prices ranging from 
$.02 to $5.12 per share which expire at various dates through April 2000. 
Pursuant to the research and development collaboration agreement with Aventis 
Research and Technologies, an affiliate of Hoechst AG ("Aventis"), (see note 
10), the Company will be issuing to Aventis a warrant to purchase 120,238 
shares of common stock exercisable through March 2004 at an exercise price of 
$8.75 per share.

    STOCK OPTION PLANS

    Under the Company's 1993 Stock Option Plan, as amended in April 1995, 
654,671 shares of common stock were reserved for issuance upon exercise of 
stock options granted by the Company. In April 1995, the Board of Directors 
adopted the 1995 Stock Option/Stock Issuance Plan under which 333,333 shares 
of common stock were reserved for issuance. In April 1996, an additional 
650,000 shares of common stock were reserved for issuance under the 1995 
Plan. The plans provide for the grant of stock options to officers, 
directors, and employees of, and consultants and advisors to, the Company.

    In August 1997, the Board of Directors adopted the 1997 Stock Incentive 
Plan, under which 1,641,341 shares of common stock were reserved for issuance 
upon exercise of stock options granted by the Company. In November 1997, an 
additional 600,000 shares were reserved for issuance under the 1997 Plan.

    The exercise price of incentive stock options to be granted under the 
stock option plans shall not be less than 100% of the fair value of such 
shares on the date of grant. The exercise price of nonqualified stock options 
to be granted under the plans shall not be less than 85% of the fair value of 
such shares on the date of grant. Options granted prior to April 13, 1998 
(the date of the initial public offering) are generally exercisable 
immediately; however, options granted subsequent to the initial public 
offering are generally exercisable only as they vest. All shares granted 
under the Stock Option Plans generally vest at the rate of one fourth after 
one year and the remainder ratably over the remaining three years. Options 
granted have a term of up to ten years.

    As of December 31, 1998, 278,316 shares are available for future grant 
under the stock option plans. The following table summarizes stock option 
activity through December 31, 1998:

<TABLE>
<CAPTION>
                                                                            WEIGHTED
                                                                             AVERAGE
                                                                            EXERCISE
                                               NUMBER OF     PRICE PER      PRICE PER
                                                SHARES         SHARE          SHARE
                                               ---------   --------------   ---------
   <S>                                         <C>         <C>              <C>
   Outstanding at December 31, 1995             114,532    $ .02 to $ .15    $ .15
     Granted                                    665,146       $ .15          $ .15
     Exercised                                 (516,830)      $ .15          $ .15
     Cancelled                                  (28,973)      $ .15          $ .15
                                             ----------
   Outstanding at December 31, 1996             233,875    $ .02 to $ .15    $ .15
     Granted                                  1,586,223    $ .38 to $ .90    $ .89
     Exercised                               (1,381,766)   $ .15 to $ .90    $ .86
     Cancelled                                  (21,616)   $ .15 to $ .90    $ .53
                                             ----------
   Outstanding at December 31, 1997             416,716    $ .02 to $ .90    $ .60
     Granted                                  1,344,874    $ 3.00 to $10.00  $ 4.48
     Exercised                                 (248,479)   $ .15 to $  3.00  $ 1.98
     Cancelled                                 (406,910)   $ .15 to $10.00   $ 6.23
                                             ----------
   Outstanding at December 31, 1998           1,106,201    $ .02 to $  5.00  $ 2.94
                                             ----------
                                             ----------
</TABLE>

                                       F-11
<PAGE>

    As of December 31, 1998, 1,516,712 shares issued pursuant to early exercises
of options or issuable under outstanding options were vested. The Company has
the option to repurchase, at the original issue price, the unvested shares
issued pursuant to early exercise of options in the event of termination of
employment or engagement. At December 31, 1998, 1,089,707 shares issued under
the stock option plans were subject to repurchase by the Company.

    On September 25, 1998, the Compensation Committee of the Board of Directors
authorized a plan for certain option holders whereby each holder could have
exchanged all of his or her current vested and unvested options on a one-for-one
basis for new options priced at the market value as of September 25, 1998. An
aggregate of 365,463 options at an average price of $6.69 were exchanged for
options with an exercise price of $3.8125 per share. All of these replacement
options vest based on the original grant date. None of the replacement options
are exercisable until September 26, 1999, or under certain circumstances at an
earlier date.

    All replacement options are included in grants and cancellations in the
above summary of stock activity.

    The Company recognized an aggregate of $4,304,437 through April 13, 1998 as
deferred compensation for the excess of the fair value for financial statement
presentation purposes of the common stock issuable on exercise of such options
over the exercise price. The deferred compensation expense is being recognized
over the vesting period of the options. Compensation expense related to these
options was $2,181,363 and $610,924 for the years ended December 31, 1998 and
1997, respectively.

    Following is a further breakdown of the options outstanding as of December
31, 1998:

<TABLE>
<CAPTION>
                                                                                 WEIGHTED
                                             WEIGHTED                             AVERAGE
                                              AVERAGE    WEIGHTED                EXERCISE
                  RANGE OF                   REMAINING    AVERAGE                PRICE OF
                  EXERCISE        OPTIONS     LIFE IN    EXERCISE    OPTIONS      OPTIONS
                   PRICES       OUTSTANDING    YEARS       PRICE   EXERCISABLE  EXERCISABLE
                -------------   -----------  ---------   --------  -----------  -----------
                <S>             <C>          <C>         <C>       <C>          <C>
                $ .02 - $ .15     119,213        5.75      $ .15     119,213       $ .15
                $ .38 - $ .90     156,327        8.62      $ .83     156,327       $ .83
                $3.00 - $3.99     723,657        9.51      $3.65     168,811       $3.03
                $4.00 - $5.00     107,004        9.95      $4.32           -       $   -
                $ .02 - $5.00   1,106,201        9.02      $2.94     444,351       $1.48
</TABLE>

    Adjusted pro forma information regarding net loss is required by SFAS 123
and has been determined as if the Company had accounted for its employee stock
options under the fair value method of SFAS 123. The fair value for these
options was estimated at the date of grant using the Black-Scholes valuation
model for option pricing with the following assumptions for 1998, 1997 and 1996:
a risk-free interest rate of 5.75%, 6.5% and 6.5%, respectively, a dividend
yield of zero; volatility factors of the expected market price of the Company's
common stock of 65%, and a weighted average expected life of the option of five
years.

    The Black-Scholes option valuation model was developed for use in estimating
the fair value of traded options which have no vesting restrictions and are
fully transferable. In addition, option valuation models require the input of
highly subjective assumptions, including the expected stock price volatility.
Because the Company's employee stock options have characteristics significantly
different from those of traded options, and because changes in the subjective
input assumptions can materially affect the fair value estimate, in management's
opinion, the existing models do not necessarily provide a reliable single
measure of the fair value of its employee stock options.

    For purposes of adjusted pro forma disclosures, the estimated fair value of
the options is amortized to expense over the vesting period. The Company's
adjusted pro forma information is as follows (in thousands):

<TABLE>
<CAPTION>
                                                                   YEARS ENDED DECEMBER 31,
                                                              1998           1997           1996
                                                           ----------    ------------    ----------
                   <S>                                     <C>           <C>             <C>
                   Adjusted pro forma net loss             $  (21,379)   $    (11,383)   $   (7,781)
                   Adjusted pro forma net loss per         $    (1.63)   $      (8.45)   $    (8.08)
                   share
</TABLE>

    The weighted average fair value of options granted during 1998, 1997 and
1996 was $2.68, $.24 and $.01 per share, respectively.


                                       F-12
<PAGE>

    The pro forma effect on net loss for 1998, 1997 and 1996 is not necessarily
indicative of potential pro forma effects on results for future years.

    EMPLOYEE STOCK PURCHASE PLAN

    In November 1997, the Board of Directors approved the Employee Stock
Purchase Plan (the "Purchase Plan") A total of 300,000 shares of common stock
have been authorized for issuance under the Purchase Plan. The Purchase Plan
permits eligible employees of the Company to purchase shares of common stock, at
semi-annual intervals, through periodic payroll deductions. Payroll deductions
may not exceed 15% of the participant's base salary subject to certain
limitations, and the purchase price will not be less than 85% of the lower of
the fair market value of the stock at either the beginning of the applicable
"offering period" or the last day of the accumulation period. Each offering
period is 24 months long, with new offering periods commencing every six months,
and an accumulation period is six months in duration. During the year ended
December 31, 1998, 26,783 shares were issued under the Purchase Plan.

    SHARES RESERVED FOR FUTURE ISSUANCE

    The following shares of common stock are reserved for future issuance at
December 31, 1998:

<TABLE>
<CAPTION>
                   <S>                                  <C>
                   Stock options                         1,384,517
                   Employee stock purchase plan            273,217
                   Warrants                                 26,084
                                                        ----------
                                                         1,683,818
                                                        ----------
                                                        ----------
</TABLE>

    SHAREHOLDER RIGHTS PLAN

    In November 1998, the Company's Board of Directors adopted a Stockholder
Rights plan which provides for a dividend of one Preferred Stock Purchase Right
for each share of common stock to stockholders of record on November 30, 1998.
Each Right will entitle stockholders to buy one one-thousandth of a share of
Series A Participating Preferred Stock of the Company at an exercise price of
$50.00, subject to antidilution adjustments. The Rights will become exercisable
only if a person or group becomes the beneficial owner of 15% or more of the
common stock, or commences a tender or exchange offer which would result in the
offeror beneficially owning 15% or more of common stock, which is not approved
by the Company's Board of Directors. The Board of Directors is entitled to
redeem the Rights at $0.01 per Right at any time prior to the public
announcement of the existence of a 15% holder.

7.  401(K) PLAN

    The Company has a 401(k) defined contribution savings and retirement plan
(the "Plan"). The Plan is for the benefit of all qualifying employees and
permits employees voluntary contributions up to a maximum of 20% of base salary
(as defined), subject to annual limits. The Board of Directors may, at its sole
discretion, approve Company contributions. No such contributions have been made
as of December 31, 1998.

8.  NOTES RECEIVABLE FROM OFFICERS AND EMPLOYEES

    The Company has advanced funds to certain officers in connection with
various employment agreements with an outstanding balance of approximately
$240,000 at December 31, 1998, which is included in other assets. These
agreements provide for forgiveness of the advances over four-year periods. If an
individual terminates the relationship with the Company, the unforgiven portion
of the advances and any accrued interest are due and payable upon termination.
These advances are secured by second trust deeds on the personal residence of
the respective officer. In addition, there are notes receivable from certain
officers totaling approximately $1.5 million related to stock purchase
agreements. These notes are secured by shares of the Company's common stock
owned by the individual.


                                       F-13

<PAGE>

9.  INCOME TAXES

    Significant components of the Company's deferred tax assets and liabilities
as of December 31, 1998 and 1997 are shown below. A valuation allowance of
$19,250,000, of which $7,971,000 relates to 1998, as of December 31, 1998 has
been recognized to offset the deferred tax assets, as realization of such assets
is uncertain.

<TABLE>
<CAPTION>
                                                               1998          1997
                                                           -----------  ------------
            <S>                                            <C>          <C>
            Deferred tax assets:                                         
              Net operating loss carryforwards             $    14,846  $      9,120
              Research and development credits                   2,350         1,146
              Capitalized research expenses                      1,981         1,050
              Other                                                308           114
                                                           -----------  ------------
            Total deferred tax assets                           19,485        11,430
            Valuation allowance for deferred tax assets        (19,250)      (11,279)
                                                           -----------  ------------
            Net deferred tax assets                                235           151
            Deferred tax liabilities:                                    
              Depreciation                                        (235)         (151)
                                                           -----------  ------------
            Net deferred tax assets                        $        --  $         --
                                                           -----------  ------------
                                                           -----------  ------------
</TABLE>

    At December 31, 1998, the Company has federal and California net 
operating loss carryforwards of approximately $41,383,000 and $6,298,000, 
respectively. The difference between the federal and California tax loss 
carryforwards is primarily attributable to the capitalization of research and 
development expenses for California tax purposes and the fifty percent 
limitation on California loss carryforwards. The federal tax loss 
carryforwards will begin expiring in 2006 unless previously utilized. The 
California tax loss carryforwards will continue to expire in 1999, unless 
previously utilized. The Company also has federal and California research and 
development tax credit carryforwards of approximately $1,706,000 and 
$990,000, respectively, which will begin expiring in 2007 unless previously 
utilized.

    Under Sections 382 and 383 of the Internal Revenue Code, the annual use 
of the Company's net operating loss and credit carryforwards may be limited 
because of cumulative changes in ownership of more than 50% which occurred 
during 1995 and 1997. However, the Company does not believe such limitations 
will have a material impact upon the ultimate utilization of these 
carryforwards.

10.  SPONSORED RESEARCH AGREEMENTS

    BECTON, DICKINSON AND COMPANY

    In May 1997, Becton, Dickinson and Company and Nanogen entered into a 
Collaborative Research and Development Agreement to develop products 
utilizing Nanogen's technology to detect microbial agents causing infectious 
disease and to determine their antibiotic susceptibility or resistance (the 
"Prior R&D Agreement"). In connection with the Prior R&D Agreement, Nanogen 
entered into a Series D Preferred Stock Purchase Agreement with Becton 
Dickinson pursuant to which Becton Dickinson purchased 1,000,000 shares of 
Nanogen's Series D Preferred Stock for $6.0 million. In addition, Becton 
Dickinson agreed, pursuant to the stock purchase agreement, to purchase 
common stock worth an aggregate of $6.0 million, at the initial public 
offering price, upon the completion of the offering. This purchase was made 
as part of a private placement concurrent with the offering.

    As of October 1, 1997, Becton Dickinson and Nanogen entered into new 
agreements which superseded the Prior R&D Agreement. Pursuant to a Master 
Agreement entered into between the parties (the "Master Agreement"), Becton 
Dickinson and Nanogen agreed to form The Nanogen/Becton Dickinson 
Partnership, a Delaware general partnership (the "Partnership") to develop 
and commercialize certain products in the field of IN VITRO nucleic 
acid-based diagnostic and monitoring technologies. NanoVenture LLC, a 
Delaware limited liability company wholly-owned by Nanogen ("NanoVenture") 
and Becton Dickinson Venture LLC, a Delaware limited liability company 
wholly-owned by Becton Dickinson ("Becton Dickinson Venture"), are the 
general partners of the Partnership with (a) losses allocated in proportion 
to cash funding, (b) profits shared equally, and (c) distributions allocated 
60% to Becton Dickinson Venture and 40% to NanoVenture until partner 
contributions are equalized and thereafter distributions shared equally. 
Pursuant to a General Partnership Agreement between NanoVenture and Becton 
Dickinson Venture, Becton Dickinson and Nanogen have contributed to the 
Partnership their respective rights under the Prior R&D Agreement, certain 
Intellectual Property Licenses and, as of December 31, 1998, cash in the 
aggregate of approximately $4.6 million, of which approximately $4.0 million 
was paid by Becton Dickinson and 


                                       F-14
<PAGE>

approximately $600,000 was paid by Nanogen. The amounts paid by Nanogen have 
been recorded as Nanogen's share of the joint venture's loss for the year 
ended December 31, 1998. The General Partnership Agreement also contemplates 
additional research funding aggregating approximately $17.7 million, of which 
$5.2 million is to be paid by Nanogen, during the period from January 1, 1999 
through April 1, 2001, conditioned upon the achievement of certain 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 addition to the above-described payments, Becton Dickinson and 
Nanogen have agreed to contribute certain additional amounts to fund 
marketing and manufacturing startup.

    Revenues are recognized under the agreements as expenses are incurred, 
and totaled approximately $2.5 million and $1.2 million for the years ended 
December 31, 1998 and 1997, respectively.

    HOECHST AG

    In December 1997, the Company entered into an agreement with Aventis 
Research and Technologies, an affiliate of Hoechst AG ("Aventis"), for an 
exclusive research and development collaboration and the establishment of a 
joint venture relating to new tools in molecular recognition and Nanogen's 
technology. Aventis also purchased common stock worth an aggregate of $10.0 
million, at the offering price, in the private placement in April 1998.

    Revenue is recognized under the agreement as expenses are incurred, and 
totaled approximately $2.1 million for the year ended December 31, 1998. 
Funding received in advance of incurred expenses is recorded as deferred 
revenue until the expenses are incurred, and totaled $2.9 million at December 
31, 1998.

    In December 1998, the Company entered into a Collaborative Research and 
Development Agreement which, among other things, extended the guaranteed term 
of the research program from two to three years. As a result of the signing 
of this agreement, the Company will be issuing to Aventis a warrant to 
purchase 120,238 shares of common stock exercisable through March 2004 at an 
exercise price of $8.75 per share.

    ELAN CORPORATION, PLC

    In December 1997, the Company entered into an agreement with Elan 
Corporation, plc ("Elan") for a non-exclusive research and development 
agreement for the development of genomics and gene expression research tools. 
Pursuant to the agreement, Elan purchased Company common stock worth an 
aggregate of $5.0 million, at the initial public offering price, in the 
private placement in April 1998.

    Revenue is recognized under the agreement as expenses are incurred, and 
totaled approximately $929,000 for the year ended December 31, 1998.

11. CONTRACT AND GRANT REVENUE

    In September 1998, the Company was awarded a contract by the Space and 
Naval Warfare Systems Center San Diego ("SSC San Diego") for the Defense 
Advance Research Projects Agency in an amount that could total in excess of 
$7 million over the next five years. The contract award which was made by SSC 
San Diego for the Defense Advance Research Projects Agency includes over $2 
million to be paid during the first two years, and options to extend the 
program for up to an additional three years that would pay the Company up to 
an additional $4.8 million. The goal of the program is to create an advanced 
miniaturized lab for biological warfare defense applications.

    In July 1998, the Company received a grant of $500,000 from the National 
Institute of Justice. This grant was the Company's second grant awarded under 
the U.S. Department of Justice, Office of Justice Programs to enable the 
Company to continue its work in the development of a portable microchip 
array-based genetic detector for rapid forensic DNA testing and 
identification at the crime scene.




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