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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                            ------------------------
 
                                   FORM 10-K
 
(MARK ONE)
 
     [X]   ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
        SECURITIES EXCHANGE ACT OF 1934
 
                    FOR THE FISCAL YEAR ENDED JUNE 30, 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 0-28272
 
                                  AVIGEN, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)
 
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            DELAWARE                          13-3647113
  (STATE OR OTHER JURISDICTION             (I.R.S. EMPLOYER
OF INCORPORATION OR ORGANIZATION)         IDENTIFICATION NO.)
</TABLE>
 
         1201 HARBOR BAY PARKWAY, SUITE 1000, ALAMEDA, CALIFORNIA 94502
             (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES AND ZIP CODE)
 
                                 (510) 748-7150
              (REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE)
 
          SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:
 
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       TITLE OF EACH CLASS          NAME OF EACH EXCHANGE ON WHICH
                                              REGISTERED
              NONE
</TABLE>
 
          SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:
 
                         COMMON STOCK, $.001 PAR VALUE
                                (TITLE OF CLASS)
 
     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Sections 13 of 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 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 amendments to
this Form 10-K.  [X]
 
     The aggregate market value of the voting stock held by nonaffiliates of the
registrant as of September 21, 1998, was approximately $22,840,728 based upon
the closing sale price of the registrant's Common Stock as reported on the
NASDAQ National Market System on such date. The number of outstanding shares of
the Registrant's Common Stock as of September 21, 1998 was 7,309,033.
 
                      DOCUMENTS INCORPORATED BY REFERENCE
 
     Parts of the following documents are incorporated by reference into Parts
III and IV of this Form 10-K Report: The definitive Proxy Statement for the
Registrant's Annual Meeting of Stockholders scheduled to be held on November 19,
1998.
 
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                           ANNUAL REPORT ON FORM 10-K
                    FOR THE FISCAL YEAR ENDED JUNE 30, 1998
 
                               TABLE OF CONTENTS
 
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PART I
  Item 1.   Business....................................................    7
  Item 2.   Properties..................................................   19
  Item 3.   Legal Proceedings...........................................   19
  Item 4.   Submission of Matters to a Vote of Security Holders.........   19
 
PART II
  Item 5.   Market for Registrant's Common Equity and Related              19
              Stockholder Matters.......................................
  Item 6.   Selected Financial Data.....................................   20
  Item 7.   Management's Discussion and Analysis of Financial Condition    21
              and Results of Operations.................................
  Item 8.   Financial Statements and Supplementary Data.................   23
  Item 9.   Changes in and Disagreements with Accountants on Accounting    23
              and Financial Disclosure..................................
 
PART III
  Item 10.  Directors and Executive Officers of the Registrant..........   23
  Item 11.  Executive Compensation......................................   23
  Item 12.  Security Ownership of Certain Beneficial Owners and            23
              Management................................................
  Item 13.  Certain Relationships and Related Transactions..............   23
 
PART IV
  Item 14.  Exhibits, Financial Statement Schedules and Reports on Form    23
              8-K.......................................................
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     Except for the historical information contained herein, this report
contains forward-looking statements that involve risks and uncertainties. The
Company's actual results could differ materially from those discussed here.
Factors that could cause or contribute to such differences include, but are not
limited to, those discussed under the heading "Risk Factors."
 
                                     PART I
 
                                  RISK FACTORS
 
     This section briefly discusses certain risks that should be considered by
stockholders and prospective investors in the Company. Many of these risks are
discussed in other contexts in other sections of this report.
 
EARLY STAGE OF DEVELOPMENT; TECHNOLOGICAL UNCERTAINTY
 
     Gene therapy is a new and rapidly evolving technology. To date, there has
been only limited research and development in gene therapy using AAV vectors.
The Company is not aware of any gene therapy products which have obtained
marketing approval from the United States Food and Drug Administration ("FDA").
Because there is only limited research regarding the safety and efficacy of AAV
vectors, the Company believes that clinical trials will proceed more slowly than
clinical trials involving traditional drugs and biologics.
 
     Avigen is at an early stage of development. All of the Company's potential
products are in research or early preclinical development. There can be no
assurance that the Company's research and development activities will be
completed successfully or will support the initiation of clinical trials or that
any proposed products will prove to be efficacious or safe. Before obtaining
regulatory approval for the commercial sale of any of its products under
development, the Company must demonstrate through preclinical studies and
clinical trials that the proposed product is safe and efficacious for its
intended use. None of the Company's proposed products has been tested in humans.
There can be no assurance that the Company will not encounter problems with the
clinical trials which will require the Company to delay, suspend or terminate
such trials. All of the Company's products in research and development may prove
to have undesirable and unintended side effects or other characteristics that
may prevent or limit their commercial use. Even if successfully developed, there
can be no assurance that any potential products will be cleared for marketing by
United States or foreign regulatory authorities or that such products can be
manufactured at acceptable cost or that any approved products can be
successfully marketed. Products resulting from the Company's research and
development efforts, if any, are not expected to be commercially available and
revenues from the sale of any such products are not expected for at least the
next several years.
 
HISTORY OF LOSSES
 
     To date, the Company has been engaged in research and development
activities and has not generated any revenues from product sales. The process of
developing the Company's products will require significant research and
development, preclinical testing and clinical trials, as well as regulatory
approval. These activities, together with the Company's general and
administrative expenses, are expected to result in operating losses for the
foreseeable future. The Company's ability to achieve profitability is dependent,
in part, on its ability to successfully complete development of its proposed
products, obtain required regulatory approvals and manufacture and market its
products directly or through partners. There can be no assurance that the
Company will achieve revenues or profitability in the future.
 
FUTURE CAPITAL NEEDS; UNCERTAINTY OF ADDITIONAL FUNDING
 
     The Company will require substantial additional funding in order to
complete the research and development activities currently contemplated and to
commercialize its proposed products. The Company anticipates that its existing
capital resources will be adequate to fund its capital needs for at least the
next 12 months. The Company's future capital requirements will depend on many
factors, including continued scientific progress in research and development
programs, the scope and results of preclinical studies and clinical trials, the
time and costs involved in obtaining regulatory approvals, the costs involved in
filing,
 
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prosecuting and enforcing patent claims, competing technological developments,
the cost of manufacturing scale-up, the cost of commercialization activities and
other factors which may not be within the Company's control.
 
     The Company intends to seek additional funding through public or private
equity or debt financing, when market conditions allow. If additional funds are
raised by issuing equity securities, further dilution to the existing
stockholders may result. There can be no assurance that the Company will be able
to enter into such collaborative or financing arrangements on acceptable terms
or at all. Without such additional funding, the Company may be required to
delay, reduce the scope of or eliminate one or more of its research or
development programs.
 
     The Company's common stock is traded on the Nasdaq National Market
("Nasdaq"). In order to maintain its listing on Nasdaq, the Company must
maintain net tangible assets, market capitalization and public float at
specified levels, and generally must maintain a minimum bid price of $1.00 per
share. The Company believes that maintaining its listing on Nasdaq is central to
its ability to raise additional funds as well as to provide liquidity to
investors. The Company failed to meet the Nasdaq net tangible asset listing
requirement at June 30, 1998. The Company will be required to generate
sufficient revenue or raise additional capital to maintain Nasdaq listing
requirements through second fiscal quarter 1999.
 
NEED FOR ESTABLISHMENT OF CORPORATE PARTNER RELATIONSHIPS
 
     The Company does not currently have a corporate partner relationship with
respect to any of its technologies or potential products. Given the very high
cost of funding clinical trials and bringing a proposed product through the
governmental approval process to the commercial market, the Company believes
that successful development and commercialization of its technologies and
products will depend in large part on the establishment of one or more such
relationships. There can be no assurance that the Company will be able to
establish such relationships on favorable terms, if at all. In addition, the
failure to raise needed future capital could put the Company at a disadvantage
with respect to negotiating favorable terms with such potential corporate
partners.
 
NEED TO OBTAIN RIGHTS TO PROPRIETARY GENES AND TECHNOLOGY
 
     A number of the gene sequences or proteins encoded by certain of those
sequences that the Company is investigating or may use in its products are or
may become patented by others. As a result, the Company may be required to
obtain licenses to such gene sequences or proteins or other technology in order
to test, use or market such products. For example, in connection with its anemia
program, the Company anticipates that it may need to obtain a license to a gene
for erythropoietin. There can be no assurance that the Company will be able to
obtain such a license on terms favorable to the Company, if at all. In
connection with the Company's efforts to obtain rights to such gene sequences or
proteins, the Company may find it necessary to convey rights to its technology
to others.
 
     The Company has entered into agreements for the license from third parties
of certain technologies related to its gene therapy product development
programs. Certain of these license agreements provide for the achievement of
development milestones at various times beginning in February 1997, which were
amended extending the date to December 31, 1997. In the event the Company fails
to achieve such milestones or to obtain extensions, certain of the license
agreements may be terminated by the licensor with relatively short notice to the
Company. Termination of any of the Company's license agreements could have a
material adverse effect on the Company's business.
 
     Some of the Company's gene therapy products may require the use of multiple
proprietary technologies. Consequently, the Company may be required to make
cumulative royalty payments to several third parties. Such cumulative royalties
could be commercially prohibitive. While the Company believes the third parties
will be motivated to adjust the royalty structure under such circumstances,
there can be no assurance that the Company will be able to successfully
negotiate such royalty adjustments.
 
UNCERTAINTY OF MARKET ACCEPTANCE
 
     The Company's success is dependent on acceptance of its gene therapy
products. The Company believes that recommendations by physicians and health
care payors will be essential for market acceptance of its gene
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therapy products. In the past, concerns have arisen regarding the potential
safety and efficacy of gene therapy products derived from pathogenic viruses
such as retroviruses and adenoviruses. While the Company's proposed gene therapy
products are derived from AAV which is a non-pathogenic virus, there can be no
assurance that physicians and health care payors will conclude that the
technology is safe. In addition, health care payors can indirectly affect the
attractiveness of the Company's proposed products by regulating the maximum
amount of reimbursement they will provide for such proposed products. There can
be no assurance that the Company's products will achieve significant market
acceptance among patients, physicians or third party payors, even if necessary
regulatory and reimbursement approvals are obtained. Failure to achieve
significant market acceptance will have a material adverse effect on the
Company's business, financial condition and results of operations.
 
GOVERNMENT REGULATION
 
     The production and marketing of the Company's proposed products and its
ongoing research and development activities are subject to extensive regulation
by governmental authorities in the United States and foreign countries. At the
present time, the Company believes that its products will be regulated as
biologics by the FDA and comparable foreign regulatory bodies. Gene therapy is,
however, a relatively new technology and has not been extensively tested in
humans. The regulatory requirements governing gene therapy products are
uncertain and are subject to change. No gene therapy products have been approved
to date in the United States or any foreign country. Failure to comply with
applicable FDA or other applicable regulatory requirements may result in
criminal prosecution, civil penalties, recall or seizure of products, total or
partial suspension of production or injunction, as well as other regulatory
action against the Company.
 
     The Company is currently conducting preclinical studies and is planning
clinical trials of its AAV vectors. Prior to marketing in the United States, any
drug developed by the Company must undergo rigorous preclinical and clinical
testing and an extensive regulatory approval process implemented by the FDA
under the federal Food, Drug and Cosmetic Act. Satisfaction of such regulatory
requirements, which includes satisfying the FDA that the product is both safe
and efficacious, typically takes several years or more depending on the type,
complexity and novelty of the product, and requires a substantial commitment of
resources. The Company may encounter significant delays or excessive costs in
its efforts to secure regulatory approvals, particularly because gene therapy is
a novel method of treatment and regulatory requirements are evolving and
uncertain. Preclinical studies must be conducted in conformance with the FDA's
Good Laboratory Practices regulations. Before commencing clinical trials, the
Company must submit to and receive FDA authorization of an investigational new
drug application ("IND"). There can be no assurance that submission of an IND
would result in FDA authorization to commence clinical trials.
 
     Clinical trials must meet FDA regulatory requirements for Institutional
Review Board ("IRB") oversight and informed consent and good clinical practice
regulations. The Company has limited experience in conducting preclinical
studies and no experience in conducting clinical trials necessary to obtain
regulatory approval. There can be no assurance that those clinical trials can be
conducted at preferred sites, sufficient test subjects can be recruited or
clinical trials will be started or completed successfully in a timely fashion,
if at all. Furthermore, the FDA may suspend clinical trials at any time if it
believes the subjects participating in such trials are being exposed to
unacceptable health risks or if it finds deficiencies in the IND or conduct of
the investigation. There can be no assurance that the Company will not encounter
problems in clinical trials which cause the Company or the FDA to delay, suspend
or terminate such trials.
 
     In addition to the FDA requirements, the National Institutes of Health
("NIH") has established guidelines for research involving recombinant DNA
molecules, which are utilized by the Company in its research. These guidelines
apply to recombinant DNA research which is conducted at or supported by the NIH.
Under current guidelines, proposals to conduct clinical research involving gene
therapy at institutions supported by the NIH must be approved by the NIH's
Recombinant DNA Advisory Committee.
 
     There can be no assurance that any product developed by the Company will
prove to be safe and efficacious in clinical trials or will meet all of the
applicable regulatory requirements necessary to receive marketing approval. Data
obtained from preclinical and clinical activities are susceptible to varying
interpretations which could delay, limit or prevent regulatory approvals. If
regulatory approval is granted for a product, such approval will be limited to
those disease states and conditions for which the product is useful, as
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demonstrated through clinical trials. Furthermore, approval may require ongoing
requirements for postmarketing studies. Even if a product is approved for
marketing, the product, its manufacturer and its manufacturing facilities are
continuously subject to review and periodic inspections. Discovery of previously
unknown problems with a product, manufacturer or facility may result in
restrictions on such product or manufacturer, including withdrawal of the
product from the market.
 
     In order to market its products outside of the United States, the Company
also must comply with numerous and varying foreign regulatory requirements,
implemented by foreign health authorities, governing the design and conduct of
human clinical trials and marketing approval. The approval procedure varies
among countries and can involve additional testing, and the time required to
obtain approval may differ from that required to obtain FDA approval. The
foreign regulatory approval process includes all of the risks associated with
obtaining FDA approval set forth above, and approval by the FDA does not ensure
approval by the health authorities of any other country.
 
UNCERTAINTY OF PRODUCT PRICING AND THIRD PARTY REIMBURSEMENT
 
     The business and financial condition of biotechnology companies such as the
Company are affected by the efforts of government and third party payors to
contain or reduce the cost of health care through various means. In the United
States, there have been and will continue to be a number of federal and state
proposals to implement government control on pricing. In addition, the emphasis
on managed care in the United States has increased and will continue to increase
the pressure on the pricing of pharmaceutical products. While the Company cannot
predict whether any legislative or regulatory proposals will be adopted or the
effect such proposals or managed care efforts may have on its business, the
announcement of such proposals or efforts could have a material adverse effect
on the Company's ability to raise capital, and the adoption of such proposals
could have a material adverse effect on the Company's business, financial
condition and results of operations. In addition, in both the United States and
elsewhere, sales of medical products and treatments are dependent, in part, on
the availability of reimbursement to the consumer from third-party payors, such
as government and private insurance plans. Third-party payors are increasingly
challenging the prices charged for medical products and services. If the Company
succeeds in bringing its proposed products to the market, there can be no
assurance that these products will be considered cost-effective and that
reimbursement to the consumer will be available or will be sufficient to allow
the Company to sell its products on a competitive basis.
 
COMPETITION
 
     The field of gene therapy is new and rapidly evolving, and is expected to
undergo significant technological change in the future. The Company believes its
primary competitors in the AAV gene therapy market are Genetic Therapy, Inc.
(acquired by Sandoz, Ltd.), Genzyme Corporation, and Targeted Genetics
Corporation. In addition, competition from fully integrated pharmaceutical
companies and other biotechnology companies is expected to increase,
particularly as large pharmaceutical companies acquire smaller gene therapy
companies. Most of these companies have significantly greater financial
resources and expertise than the Company in research and development,
preclinical studies and clinical trials, obtaining regulatory approvals,
manufacturing, marketing and distribution. One of these companies is supporting
clinical studies for use of AAV vectors in the treatment of cystic fibrosis.
Smaller companies may also prove to be significant competitors, particularly
through collaborative arrangements with large pharmaceutical companies. Academic
institutions, governmental agencies and other public and private research
organizations also conduct research, seek patent protection and establish
collaborative arrangements for product development and marketing. In addition,
these companies and institutions compete with the Company in recruiting and
retaining highly qualified scientific and management personnel.
 
     The Company is aware that other companies are conducting clinical trials
and preclinical studies for viral and non-viral gene therapy products. These
companies include Cell Genesys, Inc., GeneMedicine, Inc., Systemix, Inc.,
Viagene, Inc. (acquired by Chiron Corporation) and Vical Incorporated. Avigen
believes the primary competitive factors for success in the gene therapy field
will be product efficacy, safety, manufacturing capability, the timing and scope
of regulatory approvals, the timing of market introduction, marketing and sales
capability, reimbursement coverage, price and patent position. There can be no
assurance that the
 
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Company's competitors will not develop more effective or more affordable
products, or achieve earlier product commercialization than the Company.
 
UNCERTAIN PROTECTION OF INTELLECTUAL PROPERTY; POSSIBLE CLAIMS OF OTHERS
 
     To date, the Company has filed a number of patent applications in the
United States relating to the Company's technologies. In addition, the Company
has acquired exclusive and non-exclusive licenses to certain issued patents and
pending patent applications. There is no assurance that patents will issue from
these applications or that any patent will issue on technology arising from
additional research or, if patents do issue, that claims allowed will be
sufficient to protect the Company's technologies.
 
     The patent application process takes several years and entails considerable
expense. The failure to obtain patent protection on the technologies underlying
the Company's proposed products may have a material adverse effect on the
Company's competitive position and business prospects. Important legal issues
remain to be resolved as to the scope of patent protection for biotechnology
products, and the Company expects that administrative proceedings, litigation or
both will be necessary to determine the validity and scope of its and others'
biotechnology products. Such proceedings or litigation may require a significant
commitment of the Company's resources in the future. If patents can be obtained,
there can be no assurance that any such patents will provide the Company with
any competitive advantage. For example, there can be no assurance that others
will not independently develop similar technologies, others will not duplicate
any technology developed by the Company, or any such patent will not be
invalidated in litigation. In addition, two of the Company's patent applications
are co-owned with co-inventors. Under the terms of agreements with such
co-inventors, the Company has an option to obtain an exclusive, worldwide,
transferable, royalty-bearing license for such technology, and is currently in
discussions with one of the co-inventors to obtain such a license. In the event
the Company is unable to negotiate exclusive rights to such co-owned technology,
each co-inventor may have rights to independently make, use, offer to sell or
sell the patented technology. Commercialization, assignment or licensing of such
technology by a co-inventor could have a material adverse effect on the
Company's business, financial condition and results of operations.
 
     There can be no assurance that third parties will not assert patent or
other intellectual property infringement claims against the Company with respect
to its products or technology or other matters. There may be third-party patents
and other intellectual property relevant to the Company's products and
technology which are not known to the Company. Although no third party has
asserted that the Company is infringing such third party's patent rights or
other intellectual property, there can be no assurance that litigation asserting
such claims will not be initiated, that the Company would prevail in any such
litigation, or that the Company would be able to obtain any necessary licenses
on reasonable terms, if at all. Any such claims against the Company, with or
without merit, as well as claims initiated by the Company against third parties,
can be time-consuming and expensive to defend or prosecute and to resolve. If
competitors of the Company prepare and file patent applications in the United
States that claim technology also claimed by the Company, the Company may have
to participate in interference proceedings declared by the Patent and Trademark
Office to determine priority of invention, which could result in substantial
cost to the Company, even if the outcome is favorable to the Company. In
addition, to the extent outside collaborators apply technological information
developed independently by them or by others to the Company's product
development programs or apply Avigen's technologies to other projects, disputes
may arise as to the ownership of proprietary rights to such technologies.
 
     The Company also relies on a combination of trade secret and copyright law,
employee and third-party nondisclosure agreements and other protective measures
to protect intellectual property rights pertaining to its products and
technologies. There can be no assurance that these measures will provide
meaningful protection of the Company's trade secrets, know-how or other
proprietary information in the event of any unauthorized use, misappropriation
or disclosure of such trade secrets, know-how or other proprietary information.
In addition, the laws of certain foreign countries do not protect the Company's
intellectual property rights to the same extent as do the laws of the United
States. There can be no assurance that the Company will be able to protect its
intellectual property successfully.
 
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LACK OF MANUFACTURING AND SALES AND MARKETING EXPERIENCE
 
     The Company has no experience in, and currently lacks the resources and
capability to, manufacture or market any of its proposed products on a
commercial basis. In addition, the Company's proprietary process for
manufacturing AAV vectors has not yet implemented the FDA's regulations
concerning Current Good Manufacturing Practices ("cGMP"). Initially, the Company
anticipates that it will be dependent to a significant extent on collaborative
partners or other entities for commercial scale manufacturing of its products.
In the event the Company decides to establish a commercial scale manufacturing
facility, the Company will require substantial additional funds and personnel
and will be required to comply with extensive regulations applicable to such
facility. There can be no assurance that the Company will be able to develop
adequate commercial manufacturing capabilities either on its own or through
third parties. In addition, the Company does not anticipate establishing its own
sales and marketing capabilities in the foreseeable future. There can be no
assurance that the Company will be able to develop adequate marketing
capabilities either on its own or through third parties.
 
DEPENDENCE ON KEY PERSONNEL
 
     The Company is highly dependent on certain members of its management and
research and development staff. The loss of any of these persons could have a
material adverse effect on the Company's business. In addition, the Company
relies on consultants and advisors to assist the Company in formulating its
research and development strategy. Recruiting and retaining qualified technical
and managerial personnel will also be critical to the Company's success. There
can be no assurance that the Company will be successful in attracting and
retaining skilled personnel who generally are in high demand in the
pharmaceutical and biotechnology industries. The loss of certain key employees
or the Company's inability to attract and retain other qualified employees could
have a material adverse effect on the Company's business. A majority of the
Company's scientific advisors are engaged by the Company on a consulting basis
and are employed on a full-time basis by employers other than the Company and
some have consulting or other advisory arrangements with other entities that may
conflict or compete with their obligations to the Company.
 
SIGNIFICANT PRODUCT LIABILITY RISK; LIMITED INSURANCE COVERAGE
 
     The manufacture and sale of medical products entail significant risk of
product liability claims. The Company currently does not carry product liability
insurance although it intends to obtain such coverage prior to commencing
clinical trials. There can be no assurance that such coverage will be adequate
to protect the Company from any liabilities it might incur in connection with
the use or sale of the Company's products. In addition, the Company may require
increased product liability coverage as additional products are commercialized.
Such insurance is expensive and in the future may not be available on acceptable
terms, if at all. A successful product liability claim or series of claims
brought against the Company in excess of its insurance coverage could have a
material adverse effect on the Company's business and results of operations. The
Company must indemnify certain of its licensors against any product liability
claims brought against them arising out of products developed by the Company
under these licenses.
 
HAZARDOUS MATERIALS
 
     The Company's research and development efforts involve the use of hazardous
materials, chemicals and various radioactive compounds. The Company is subject
to federal, state and local laws and regulations governing the storage, use, and
disposal of such materials and certain waste products. Although the Company
believes that its safety procedures for handling and disposing of such materials
comply with the standards prescribed by federal, state and local regulations,
the risk of accidental contamination or injury from these materials cannot be
completely eliminated. In the event of an accident, the Company could be held
liable for any damages that result and any such liability could exceed the
resources of the Company. The Company may incur substantial costs to comply with
environmental regulations if the Company develops its own commercial
manufacturing facility.
 
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CONTROL BY EXISTING STOCKHOLDERS; ANTI-TAKEOVER EFFECTS OF CERTAIN CHARTER
PROVISIONS AND DELAWARE LAW
 
     The Company's officers, directors and principal stockholders beneficially
own approximately 17% of the Company's Common Stock. As a result, such persons
may have the ability to effectively control the Company and direct its affairs
and business. Such concentration of ownership may also have the effect of
delaying, deferring or preventing a change in control of the Company. In
addition, the Company's Board of Directors have the authority to issue up to
5,000,000 shares of Preferred Stock and to determine the price, rights,
preferences and privileges of those shares without any further vote or action by
the stockholders. The rights of the holders of Common Stock will be subject to,
and may be materially adversely affected by, the rights of the holders of any
Preferred Stock that may be issued in the future. The issuance of Preferred
Stock could have the effect of making it more difficult for a third party to
acquire a majority of the outstanding voting stock of the Company. The Company
has no present plans to issue shares of Preferred Stock. Furthermore, certain
provisions of the Company's Restated Certificate of Incorporation may have the
effect of delaying or preventing changes in control or management of the
Company, which could adversely affect the market price of the Company's Common
Stock. In addition, the Company is subject to the provisions of Section 203 of
the Delaware General Corporation Law (the "Delaware Law"), an anti-takeover law.
 
VOLATILITY OF STOCK PRICE
 
     The Company believes that various factors, including announcements of
technological innovations or regulatory approvals, results of clinical trials,
announcements of new products by the Company or by its competitors, healthcare
or reimbursement policy changes by governments or insurance companies,
developments in relationships with corporate partners or a change in securities
analysts' recommendations, may cause the market price of the Common Stock to
fluctuate, perhaps substantially. In addition, in recent years the stock market
in general, and the shares of biotechnology and healthcare companies in
particular, have experienced extreme price fluctuations. These broad market and
industry fluctuations may materially adversely affect the market price of the
Company's Common Stock. Beginning November 19, 1996, contractual restrictions on
the sale of approximately 3,646,559 shares of Common Stock otherwise eligible
for sale subject to compliance with Rule 144 or Rule 701 expire.
 
ITEM 1. BUSINESS
 
THE COMPANY
 
     Avigen is a leader in the development of gene therapy products derived from
adeno-associated virus ("AAV") for the treatment of inherited and acquired
diseases. The Company's proposed gene therapy products are designed for in vivo
administration to achieve the production of therapeutic proteins within the
body. The Company is developing two broad-based proprietary gene delivery
technologies: AAV vectors and the Targeted Vector Integration ("TVI") system.
The Company believes AAV vectors can be used to deliver genes for the treatment
of hemophilia, thalassemia, hyperlipidemia, neural diseases and metabolic
storage diseases.
 
     AAV Vectors. The Company's gene therapy products are based on gene delivery
systems called vectors. AAV vectors are derived from AAV, a common
non-pathogenic human virus, and take advantage of the natural efficiency with
which viruses deliver genes to cells. To produce an AAV vector, the virus is
modified by removing the viral genes and replacing them with genes for
therapeutic proteins. The Company believes that AAV vectors combine desirable
properties of viral and non-viral vectors and may offer several potential
advantages over other gene therapy vectors. These advantages include efficient
delivery of genes to both dividing and non-dividing target cells, absence of
viral genes that may be responsible for causing an undesirable immune response,
in vivo administration to patients, higher levels of gene expression and
improved stability allowing AAV vectors to be stored and handled like more
traditional pharmaceutical products. Due to the complex replication cycle of the
natural virus, AAV vectors have been difficult to produce. Avigen believes that
its proprietary manufacturing process will simplify manufacturing and
purification and achieve increased yield of high purity AAV vectors.
 
                                        7
<PAGE>   10
 
     In spite of the potential advantages, the use of AAV vectors for gene
therapy also presents potential disadvantages. Since the genome of the natural
AAV virus is relatively small, the amount of the genetic material that can be
included in an AAV vector is limited. Therefore, large genes cannot be delivered
by AAV vectors. In addition, in vivo administration of AAV vectors may result in
the production of antibodies which may limit the effectiveness of repeat dosing
of these vectors. Furthermore, direct administration of AAV vectors may result
in their distribution to inappropriate tissues.
 
     Product Development. Based on encouraging results in animal models, the
Company has initiated two preclinical development programs using AAV vectors for
the treatment of hemophilia and thalassemia. Additionally, the Company has a
number of research programs and collaborations intended to generate product
development candidates for hyperlipidemia, neural disease and metabolic storage
diseases. Avigen believes that the number of potential applications for gene
therapy will increase significantly as advances are made in the area of
genomics. These advances are enabling scientists to link diseases to specific
gene defects. As more genes are discovered, the need for improved gene delivery
technologie is expected to increase. With the identification of new
disease-related genes, the Company believes that its AAV vectors will provide it
with significant opportunities for new gene therapy products.
 
     Corporate Partnering Opportunities. The Company is seeking to develop
long-term strategic collaborations with pharmaceutical companies that can
provide funding for research and development activities and clinical trials as
well as access to complementary technologies, including gene sequences. The
Company believes that its proprietary gene delivery technologie can be used to
deliver a number of different genes, giving rise to multiple product and
corporate partnering opportunities.
 
GENE THERAPY BACKGROUND
 
     Gene therapy is an approach to the treatment of inherited and acquired
diseases whereby genes are delivered into patients' cells in order to direct the
cells to produce therapeutic proteins. Genes are regions of DNA that contain the
instructions that direct cells to produce proteins, one of the basic building
blocks of all cells. Each cell in the body has the ability to produce proteins
necessary for cellular structure, growth and function. The process that results
in protein production by the cell is known as gene expression. By directing the
cells to produce proteins, gene therapy offers the opportunity to correct
defects or diseases at the molecular level. All gene therapy approaches contain
three key components: (i) the vector, (ii) the gene cassette, and (iii) the
target cell.
 
     Vectors. One of the most critical factors for the success of gene therapy
products is the development of vectors that can practically, efficiently and
safely deliver genes into cells. The process of gene transfer may be
accomplished in vivo (by administering the vector directly to patients) or ex
vivo (by removing patients' cells and combining them with vector). Viral vectors
are derived from naturally occurring viruses. Non-viral vectors are produced by
standard recombinant DNA techniques.
 
     Viral vectors take advantage of the natural efficiency with which viruses
transport their own genetic information into cells. Viral vectors are
constructed by removing some or all of the viral genes and replacing them with a
gene cassette. Viral vectors have been the most extensively studied method of
gene delivery, and most gene therapy applications currently undergoing clinical
evaluation involve the use of viral vectors. However, viral vectors currently
under clinical investigation have limitations which may affect their safety or
efficacy. Viral vectors based on retroviruses ("retroviral vectors"), for
example, require that target cells be dividing or multiplying to achieve gene
delivery. Because most target cells in the body are not dividing or divide very
slowly and because retroviruses become rapidly inactivated in the blood, most
clinical applications currently under evaluation employing retroviral vectors
involve a complex and expensive procedure whereby patient cells are removed and
the gene is delivered to these cells ex vivo.
 
     Another type of viral vector is derived from adenovirus. Adenoviral vectors
are capable of efficiently delivering genes to dividing and non-dividing cells.
However, adenoviral vectors contain and express genes from the naturally
occurring virus, and as a result, the body's immune system is triggered
following their administration. This immune response is believed to limit the
length of time that gene expression can be maintained in the target cell.
                                        8
<PAGE>   11
 
     Additional safety issues have been raised by the use of retroviral and
adenoviral vectors since both vectors are derived from pathogenic viruses.
During the manufacture of these vectors, there is a possibility of generating a
small amount of the natural virus. Although considered a low risk, such a
possibility necessitates additional costly product testing. In addition,
retroviral vectors randomly integrate the gene cassette into the target cell.
Any gene therapy approach that involves the random integration of genetic
material into the target cell's DNA could, theoretically, cause the activation
of another gene involved in the development of cancer or the inactivation of a
beneficial gene. It is generally believed that such events would be rare.
 
     Non-viral vectors are produced by standard recombinant DNA techniques and
are delivered to target cells either unmodified ("naked DNA") or combined with
lipids (e.g., liposomes) or proteins designed to facilitate the entry of DNA
into the cells. Because they have no components derived from viruses, they are
perceived to be safer. In addition, non-viral vectors are capable of delivering
large segments of DNA to target cells. However, non-viral vectors are relatively
inefficient at delivering genes to cells, and in general, have resulted in
temporary or low levels of gene expression in target cells.
 
     In contrast to retroviral and adenoviral vectors, AAV vectors are derived
from a non-pathogenic human virus to which the majority of the population has
been exposed. In spite of its name, AAV is genetically unrelated to adenovirus.
AAV, as it exists in nature, can only reproduce in the presence of another
virus. AAV vectors are derived from AAV by removing all of the viral genes and
replacing them with an appropriate gene cassette. The Company believes that AAV
vectors offer several potential advantages over other viral and non-viral
vectors. These advantages include efficient delivery of genes to both dividing
and non-dividing target cells, absence of viral genes that may be responsible
for causing an undesirable immune response, in vivo administration to patients,
higher levels of gene expression and improved stability allowing AAV vectors to
be manufactured, stored and handled like more traditional pharmaceutical
products. The Company believes that AAV vectors combine the desired properties
of viral and non-viral vectors and may offer a safer and more practical
alternative to the other gene therapy vectors. Two clinical trials evaluating
AAV vectors manufactured by another company for the treatment of cystic fibrosis
are currently being conducted.
 
     Gene Cassette. Packaged inside a gene therapy vector is the gene cassette,
containing the gene for a desired therapeutic protein and the control elements
which direct protein production by the cell. The design of the gene cassette
depends on the therapeutic application. The gene may be a naturally occurring
gene for a therapeutic protein (e.g., erythropoietin or factor IX), one that
sensitizes cancer cells to chemotherapy (a "suicide gene") or a man-made gene
with novel anti-viral properties. The control elements that regulate expression
of the delivered genes are equally important in the success of gene therapy
products. Certain control elements permit gene expression in many cell types
while other cell-specific control elements direct expression only in a
particular type of cell. The Company believes that inclusion of the
cell-specific control elements in a gene therapy vector may increase safety in
certain gene therapy applications by limiting gene expression to a desired organ
or tissue.
 
AVIGEN TECHNOLOGY
 
  AAV VECTORS
 
     AAV vectors are emerging as a promising gene delivery system because they
combine the efficiency with which viral vectors deliver their DNA to cells with
a potential safety profile closer to that of non-viral vectors. A major
limitation in the development of clinical applications for AAV vectors has been
the lack of an efficient production method. Current methods, in general, result
in low yields of AAV vectors and require the input of an infectious virus, most
commonly adenovirus, to initiate vector replication. The Company has developed a
proprietary manufacturing process which allows for the more efficient production
of larger quantities of AAV vectors and does not require the use of an
infectious virus, thereby eliminating some potentially harmful contaminants. The
Company believes that its process will simplify manufacturing and purification
of AAV vectors for clinical trials. In addition, the Company believes that its
proprietary process will result in a product that will be safer and, as a
result, more commercially viable than AAV vectors produced by commonly employed
methods.
 
                                        9
<PAGE>   12
 
GENE THERAPY DEVELOPMENT PROGRAMS
 
     The Company has selected its gene therapy development programs based on
experimental data that demonstrate the feasibility of gene delivery to specific
target cells. The Company believes that its technologies may be used with
several different genes, giving rise to multiple product and corporate
partnering opportunities. Avigen believes that further advances in genomics,
including the sequencing, mapping and identification of genes linked to
diseases, may offer other opportunities. The following table summarizes the
Company's current gene therapy development programs:
 
                        AAV VECTOR-GENE THERAPY PROGRAMS
 
<TABLE>
<CAPTION>
       PROGRAM           INDICATION       TARGET CELL      STATUS(1)
       -------         ---------------    ------------    -----------
<S>                    <C>                <C>             <C>

Blood Diseases         Hemophilia         Muscle/Liver    Preclinical
                       Anemia(2)          Muscle          Preclinical
Metabolic Diseases     Hyperlipidemia     Muscle          Research
                       Storage
                       Diseases           Muscle          Research
</TABLE>
 
---------------
(1) "Research" indicates activities related to designing, constructing and
    testing vectors in specific target cell types in order to evaluate gene
    expression. "Preclinical" indicates in vitro and animal studies to evaluate
    efficacy, pharmacology and toxicology.
 
(2) Includes programs utilizing delivery of an erythropoietin gene for the
    treatment of renal failure, sickle cell anemia and beta-thalassemia.
 
  BLOOD DISEASES
 
     Hemophilia. Hemophilia is a hereditary disorder characterized by the
decrease or absence of clotting factor activity in the plasma. The most common
forms are caused by deficiency in protein coagulation factor VIII ("hemophilia
A") or factor IX ("hemophilia B"). Approximately 10,000 individuals, mostly
male, are treated for hemophilia A and about 2,800 individuals are treated for
hemophilia B in the United States. Worldwide, there are about 80,000
hemophiliacs. Patients with either disease experience acute and often
life-threatening bleeding episodes and can also suffer joint deformities from
repeated bleeding into joints. Depending on the severity of disease, treatment
consists of either intermittent or chronic administration of clotting factor
which has either been purified from plasma or, more recently, a recombinant
DNA-derived protein. Transmissions of viral agents have been significantly
reduced with the increased use of highly purified or recombinant clotting
factors. The Company believes that any AAV vectors may be useful to deliver the
genes for Factor VIII or Factor IX and achieve long-term expression in vivo.
 
     Anemia. Anemia results from a variety of inherited and acquired conditions
resulting in a reduction of the number of red blood cells and hemoglobin, the
red blood cell protein that carries oxygen. In the case of sickle cell anemia
and beta-thalassemia, two inherited diseases, anemia results from the production
of inadequate or abnormal hemoglobin molecules. In acquired cases such as renal
failure, AIDS or as the result of the administration of chemotherapy for cancer,
anemia is generally due to the inadequate production of red blood cells.
 
     Erythropoietin ("EPO") is the protein produced by the kidney that
stimulates cells in the bone marrow to produce red blood cells and is involved
in the production of hemoglobin. Recombinant human EPO, a drug first developed
by Amgen, Inc., is administered several times a week by injection for the
treatment of anemia secondary to renal failure, AIDS or chemotherapy. Currently,
there are approximately 140,000 renal failure patients receiving dialysis in the
United States and an equivalent number in Europe. It is estimated that about
85,000 renal failure patients receiving dialysis are presently receiving EPO
worldwide. In addition, it is
 
                                       10
<PAGE>   13
 
estimated that approximately 50,000 AIDS patients are also currently being
treated with EPO. The incidence of anemia in the approximately 1 million cancer
patients in the United States is estimated at 14%, providing a potential
additional 140,000 patients who also may be candidates for EPO therapy.
 
     There are an estimated 60,000 patients with sickle cell anemia in the
United States. The Company believes that there are approximately 8,000 to 10,000
cases of beta-thalassemia in the United States. Currently, there is no effective
and widely available therapy for beta-thalassemia and sickle cell anemia.
Studies in animals and clinical trials in a small number of patients suggest
that administration of large doses of EPO, either alone or in combination with
other agents, in certain individuals with beta-thalassemia and sickle cell
anemia can increase the production of functional hemoglobin molecules and
perhaps ameliorate the symptoms of disease.
 
     Avigen scientists have demonstrated that biologically active levels of EPO
can be achieved in mice following a single intramuscular administration of an
AAV vector containing a gene for human EPO. Mice treated in this study showed a
dose-dependent increase in the amount of EPO in their serum and a proportional
increase in red blood cells. In this ongoing study, increased EPO levels and red
blood cell production have persisted undiminished for greater than twenty-four
months. The results of this study have not been independently verified.
 
  METABOLIC DISEASES
 
     Hyperlipidemia. Disorders of lipid metabolism contribute to a number of
common human diseases. Hyperlipidemia, characterized by elevation of cholesterol
or triglycerides in the blood, is a risk factor for atherosclerosis which leads
to heart attacks, strokes and peripheral vascular disease. Elevation of
triglycerides ("hypertriglyceridemia") often accompanies diabetes and may
contribute to the acceleration of atherosclerosis observed in that patient
population. In addition, high triglyceride levels, resulting from an underlying
genetic disease, can also lead to life-threatening pancreatitis, which is
frequently unresponsive to current therapies.
 
     Treatment of elevated lipids has been shown to decrease the risk of
atherosclerosis. There is evidence that elevated triglycerides, particularly in
combination with low HDL cholesterol ("good cholesterol") in the blood is a
substantial risk factor associated with coronary artery disease. While dietary
control and exercise are important methods to treat high cholesterol, many
individuals do not achieve adequate results with these conservative measures.
Drug therapy for high cholesterol has been successful at reducing the
complications of atherosclerosis. Although drugs to lower blood triglycerides
are widely available, medical management of this condition is often problematic
and treatment regimens are often poorly tolerated by patients. The lack of a
uniformly effective therapy for hypertriglyceridemia provides a rationale for
development of novel, alternative treatments, including gene therapy.
 
     Deficiency of the enzyme lipoprotein lipase ("LPL") is believed to be
common in patients with hypertriglyceridemia, and there may be a correlation
between decreased expression of LPL, which is normally produced in the muscle
and fat, and hypertriglyceridemia. Based on the Company's research demonstrating
that AAV vectors efficiently deliver genes to muscle resulting in sustained
protein production, the Company is working with a collaborator who intends to
conduct studies in animals to evaluate the effectiveness of delivering an AAV
vector containing the LPL gene to muscle to lower triglyceride levels.
 
     Storage diseases. Storage diseases are a diverse set of inherited disorders
characterized by a deficiency of one of several proteins that are necessary for
the function of cellular lysosomes. Lysosomes are the compartments in all cells
that process macromolecules as a part of normal turnover and tissue remodeling.
Storage diseases are characterized by abnormal cell function and cell death
resulting in a variety of clinical manifestations such as progressive neurologic
dysfunction, including mental retardation, enlarged organs or skeletal
abnormalities. Gaucher's disease and Tay-Sachs disease are two of the more
well-known examples of this class of disease.
 
                                       11
<PAGE>   14
 
     Based on the finding that long-term production of therapeutic proteins can
be obtained following the intramuscular injection of an AAV vector containing
the relevant gene, the Company has entered into collaborations to evaluate this
approach for the treatment of storage diseases. In collaboration with
investigators at The Johns Hopkins School of Medicine, the Company has initiated
studies to evaluate gene therapy for the treatment of Pompe's disease. This
disease, caused by deficient production of the enzyme, acid maltase, leads to
lethal skeletal and cardiac abnormalities in affected individuals. These
investigators intend to determine whether, following the intramuscular
administration of an AAV vector containing the acid maltase gene, the muscle
will produce a sufficient amount of this enzyme to reverse or prevent the
manifestations of this disease. Although conditions like Pompe's disease are
rare, there is currently no available treatment for these devastating diseases.
In addition, the Company believes that research on such conditions will benefit
the Company's product development efforts because the clinical endpoints are
relatively clear and measurable and the results are expected to be sufficiently
generalizable to allow for the design of AAV vector gene therapy for several
other diseases.
 
CORPORATE PARTNERING STRATEGY
 
     The Company is actively seeking to develop long-term strategic
collaborations with pharmaceutical companies that can provide funding for
research and development activities and clinical trials. The Company believes
that its technologies are proprietary and broad-based and can be used with many
different genes, giving rise to multiple product and corporate partnering
opportunities.
 
     The Company has initiated discussions with a number of pharmaceutical
companies in the United States, Europe and Asia. The Company has not entered
into any definitive agreements with respect to any corporate partnering
arrangements. Avigen's strategy is to contribute both technology and expertise
in the gene therapy field while seeking corporate partners who can provide
access to complementary technologies, including gene sequences. In addition, the
Company intends to rely on corporate partners, licensees or other entities for
marketing of its products, when and if such products achieve regulatory
approval. There can be no assurance, however, that the Company will be able to
reach satisfactory arrangements with such parties or that such arrangements will
be successful.
 
LICENSING AND RESEARCH AGREEMENTS
 
     Research Corporation Technologies. In May 1992, the Company entered into a
license agreement with Research Corporation Technologies, Inc. ("RCT") for
rights to a patent and patent application relating to a cell-specific promoter
in AAV vectors. The license is exclusive and worldwide. In consideration for the
license, the Company paid an initial license fee and issued 247,949 shares of
its Common Stock. In addition, the Company is required under the agreement to
pay RCT royalties based on net sales of products which utilize the licensed
technology, with certain minimum annual royalty payments due beginning in 1999.
Avigen must exercise its best efforts to commercially develop, promote and sell
products covered by the licensed patent rights, and is obligated to file a
product license application or a new drug application by the end of 2000. In the
event the Company fails to achieve milestones by their applicable deadlines, the
Company has the right to pay RCT additional fees of up to $250,000 to extend
certain of the deadlines for specified periods. RCT may terminate the agreement
if the Company becomes insolvent or bankrupt or fails to perform any of its
obligations under the agreement.
 
     The Johns Hopkins University. In November 1992, the Company entered into an
agreement with The Johns Hopkins University under which it issued an aggregate
of 152,702 shares of its Common Stock and agreed to make certain cash payments
in exchange for an exclusive, worldwide, royalty bearing license to a patent
application relating to certain synthetic genes which direct the production of
proteins with specific antiviral properties and which the Company believes may
be useful in infectious disease. Under the agreement, Johns Hopkins has control
over the prosecution and maintenance of the licensed patent application. The
Company is obligated to exercise its best efforts to develop and commercialize
products which utilize the subject technology. Under the terms of the agreement,
as amended, the Company is required
 
                                       12
<PAGE>   15
 
to meet the following development milestones: initiation of large animal studies
for a licensed potential product by the end of 1997, submission to the FDA of at
least one clinical protocol utilizing a licensed potential product by the end of
1998, initiation of at least one clinical study utilizing a licensed potential
product by the end of 1999 and receipt of FDA approval to market a licensed
product by the end of 2002. If the Company fails to perform any of its
obligations under the agreement, Johns Hopkins may terminate the agreement upon
60 days' written notice. For technical reasons, the Company has not met the
first milestone, and will not meet the second milestone. Johns Hopkins has taken
no action to terminate the agreement. After the completion of additional
experiments, the Company will decide whether or not to seek an extension of all
the development milestone dates.
 
     The Company has entered into other exclusive and nonexclusive license
agreements with certain research institutions and their representatives.
Although specific terms of the licenses vary, all of such licenses require the
Company to achieve certain development milestones. In addition, the agreements
require Avigen to pay certain license fees and royalties to the licensors. All
of the licenses provide for a term which extends for the life of the underlying
patent.
 
     The failure to achieve any required development milestones or to negotiate
appropriate extensions of any of the Company's license agreements or to make all
required milestone and royalty payments when due and the subsequent decision of
any such institution to terminate such license could have a material adverse
effect on the Company.
 
     The Company has also entered into agreements with certain research
institutions and corporate entities with respect to its research and development
efforts. Under such agreements the Company has provided specific vectors and
other materials for research purposes conducted at the direction of a principal
investigator. Generally, the agreements also provide that: (i) the Company
remains the sole and exclusive owner of the transferred materials; (ii)
ownership of improvements will be determined under patent law principles, based
upon the parties' relative contributions to the improvements; and (iii) the
Company has the right to prosecute patents on jointly-owned improvements.
Although specific terms of each agreement vary, the Company is generally
granted, with respect to jointly owned improvements, an irrevocable,
nonexclusive, royalty-free license and an option to negotiate in good faith an
exclusive license at royalty rates to be mutually agreed upon. There can be no
assurance that exclusive rights to any such improvements can be obtained on
terms acceptable to the Company, if at all. In addition, the Company engages
from time to time in discussions with other prospective academic partners
regarding potential research and development projects and may, in the future,
enter into arrangements in addition to those described above.
 
MANUFACTURING
 
     The Company has developed a proprietary manufacturing process for AAV
vectors. The Company believes it currently has the capacity to manufacture AAV
vectors in amounts sufficient to conduct clinical trials, but it will be
required to implement cGMP policies and procedures prior to manufacturing
material for clinical trials. The Company believes that its manufacturing
process will simplify manufacturing and purification. The processes used by the
Company are new, however, and there can be no assurance that such processes will
be feasible or cost-effective.
 
     Avigen currently does not operate manufacturing facilities for commercial
production of its gene therapy products. Avigen's strategy for the manufacture
of its gene therapy products may be to enter into alliances with pharmaceutical
and other biotechnology companies. There can be no assurance that the Company
will be able to negotiate satisfactory arrangements with such parties, that such
arrangements will be successful or that its corporate partners will be able to
develop adequate manufacturing capabilities for commercial scale production. In
the event the Company decides to establish a commercial scale manufacturing
facility, the Company will require substantial additional funds and personnel
and will be required to comply with extensive regulations applicable to such
facility.
 
                                       13
<PAGE>   16
 
GOVERNMENT REGULATION
 
     The production and marketing of the Company's proposed products and its
research and development activities are subject to regulation for safety,
efficacy and quality by numerous governmental authorities in the United States
and other countries. In the United States, pharmaceutical products are subject
to rigorous regulation by the FDA under the federal Food, Drug, and Cosmetic
Act. Biological products, in addition to being subject to certain provisions of
this act, are also regulated under the Public Health Service Act. These laws and
the regulations promulgated thereunder govern, among other things, testing,
manufacturing, safety, efficacy, labeling, storage, record keeping, advertising
and promotional practices and import and export of drugs and biological
products. In general, the Center for Biologics Evaluation and Research holds
primary responsibility for the regulation of biological products and has handled
the IND submissions of most gene therapy products to date. At the present time,
the Company believes that its products will be regulated as biologics by the FDA
and comparable foreign regulatory bodies. Gene therapy is, however, a relatively
new technology and has not been extensively tested in humans. The regulatory
requirements governing gene therapy products are uncertain and are subject to
change. No gene therapy products have been approved to date in the United States
or any foreign country.
 
     Under the NIH Guidelines for Research Involving Recombinant DNA Molecules,
clinical protocols involving human gene transfer conducted at institutions
receiving NIH funds cannot be initiated without simultaneous submission of
information describing the proposed clinical protocol to both NIH/ORDA and the
FDA. Submission to NIH/ORDA shall be for registration purposes and determination
regarding the necessity of full RAC review and approval/disapproval. Full RAC
review of an individual human gene transfer protocol can be initiated by the NIH
Director or recommended to the NIH Director by three or more RAC members or
other Federal agencies. An individual human gene transfer protocol that is
recommended for full RAC review should represent novel characteristics deserving
of public discussion. Prior to submission of a human gene transfer experiment to
NIH/ORDA, the Principal Investigator must obtain Institutional Biosafety
Committee approval from each institution that will handle recombinant DNA
material that is to be administered to human subjects and Institutional Review
Board approval from each institution in which human subjects will undergo gene
transfer. Submission of human gene transfer protocols to the FDA will be in the
form of an IND application. The review process conducted by NIH/ORDA and the FDA
is unpredictable and may result in considerable time and expense to the Company.
 
     The steps required before a new drug, including a biologic, may be marketed
in the United States generally include (i) preclinical laboratory tests and
preclinical animal studies, (ii) the submission to the FDA of an IND application
for human clinical testing, which must become effective before human clinical
trials commence, (iii) adequate and well-controlled human clinical trials to
establish the safety and efficacy of the product, (iv) the submission to the FDA
of a Product License Application and Establishment License Application
("PLA/ELA") for a biologic and (v) FDA approval of the PLA/ELA prior to any
commercial sale or shipment of the biologic. The FDA has proposed regulations
that would eliminate the separate requirement for an ELA for certain
biotechnology products, including certain recombinant DNA products, that satisfy
the regulatory definition of a "well-characterized product." The FDA, however,
has indicated that gene therapy products are not considered "well-characterized"
at this time.
 
     Domestic manufacturing establishments are subject to inspections at any
time by the FDA and must comply with cGMP regulations enforced by the FDA
through its facilities inspection program. Manufacturers of biological products
also must comply with FDA general biological product standards. In addition, the
Company must obtain a drug manufacturing license from the State of California
for any of its products administered to humans, including products intended for
clinical trials.
 
     Preclinical safety studies include laboratory evaluation of the product, as
well as animal studies to assess the potential safety and, if possible, efficacy
of the product. Preclinical studies must be conducted by laboratories that
comply with FDA regulations regarding Good Laboratory Practices. The results of
the preclinical tests, together with manufacturing information and analytical
data, are submitted to the FDA as part of an IND, which must become effective
before human clinical trials may be commenced. The IND will become automatically
effective 30 days after its receipt by the FDA unless the FDA indicates prior to
the end
 
                                       14
<PAGE>   17
 
of the 30-day period that it does not wish the trials to proceed as outlined in
the IND. In such case, the IND sponsor and the FDA must resolve any outstanding
concerns before clinical trials can proceed. There can be no assurance that
submission of an IND will result in FDA authorization to commence clinical
trials.
 
     Clinical trials must be conducted in accordance with FDA's Good Clinical
Practice regulations and must be approved by the IRB at the institution where
the study will be conducted. The IRB will consider, among other things, safety
and ethical issues, proper informed consent of the human subjects, possible
issues relating to health care costs and potential liability of the institution.
The IRB may require changes in a protocol, and there can be no assurance that an
IRB will permit any given study to be initiated or completed.
 
     Clinical trials typically are conducted in three sequential phases, but the
phases may overlap. Phase 1 typically involves the initial introduction of the
drug into patients primarily to determine the drug's metabolism,
pharmacokinetics and pharmacological actions in humans and the side effects
associated with increasing doses. Phase 2 typically involves studies in a
limited patient population to (i) determine the efficacy of the drug for
specific indications, (ii) determine dosage tolerance and optimal dosage and
(iii) further identify possible adverse effects and safety risks. If the drug is
found to be effective and to have an acceptable safety profile in Phase 2
evaluations, Phase 3 trials are undertaken to evaluate efficacy and safety
within an expanded patient population typically at geographically dispersed
clinical study sites. There can be no assurance that Phase 1, Phase 2 or Phase 3
testing will be completed successfully within any specific time period, if at
all, with respect to any of the Company's products subject to such testing.
Furthermore, the FDA may suspend clinical trials at any time on various grounds,
including a finding that patients are being exposed to an unacceptable health
risk. FDA regulations also subject sponsors of clinical investigations to
numerous regulatory requirements related to, among other things, selection of
qualified investigators, proper monitoring of investigations, record keeping and
record retention and notice to investigators and FDA of any death or adverse
serious reaction. In addition, the FDA may require post marketing clinical
studies (Phase IV) which will require extensive patient monitoring and
recordkeeping and may result in restricted marketing of the product for an
extended period of time.
 
     The results of the pharmaceutical development, preclinical studies and
clinical trials are submitted to the FDA in the form of a PLA/ELA for approval
of the manufacture, marketing and commercial shipment of the biologic. The
testing and approval process is likely to require substantial time and effort
and there can be no assurance that any approval will be granted on a timely
basis, if at all. The FDA may deny a PLA/ELA if applicable regulatory criteria
are not satisfied, require additional testing or information, or require
postmarketing testing and surveillance to monitor the safety or efficacy of a
product. Moreover, if regulatory approval of a biologic is granted, such
approval may entail limitations on the indicated uses for which it may be
marketed. Finally, product approvals may be withdrawn if compliance with
regulatory standards is not maintained or if problems occur following initial
marketing. Among the conditions for PLA/ELA approval is the requirement that the
prospective manufacturer's quality control and manufacturing procedures conform
to cGMP, which must be followed at all times. In complying with standards set
forth in these regulations, manufacturers must continue to expend time,
financial resources and effort in the area of production and quality control.
 
     In accordance with the Orphan Drug Act, the FDA may grant Orphan Drug
status to certain drugs intended to treat a "rare disease or condition" defined
as a disease or condition which affects fewer than 200,000 people in the United
States, or which affects more than 200,000 people for which the cost of
developing and marketing the drug will not be recovered from sales of the drug
in the United States. An approved Orphan Drug may provide certain benefits
including exclusive marketing rights in the United States to the drug for the
approved indication for seven years following marketing approval and federal
income tax credits for certain clinical trial expenses. The Company believes
that some of its future products may qualify for Orphan Drug status but there
can be no assurance that such products will receive FDA approval. In addition,
there is no assurance that potential benefits provided by the Orphan Drug Act
will not be significantly limited by amendment by the United States Congress
and/or reinterpretation by the FDA.
 
     For clinical investigation and marketing outside the United States, the
Company is also subject to foreign regulatory requirements governing clinical
trials and marketing approval for pharmaceutical products. In
 
                                       15
<PAGE>   18
 
Europe, the approval process for the commencement of clinical trials varies from
country to country. The foreign regulatory approval process includes all of the
risks associated with FDA approval set forth above.
 
     In addition to regulations enforced by the FDA, the Company also is subject
to regulation under the Occupational Safety and Health Act, the Environmental
Protection Act, the Toxic Substances Control Act, the Resource Conservation and
Recovery Act and other federal, state and local regulations. The Company's
research and development activities involve the controlled use of hazardous
materials, chemicals, biological materials and various radioactive compounds.
Although the Company believes that its safety procedures for handling and
disposing of such materials comply with the standards prescribed by state and
federal regulations, it could be held liable for any damages that result from
accidental contamination or injury and any such liability could exceed the
resources of the Company.
 
PATENTS AND INTELLECTUAL PROPERTY
 
     Patents and other proprietary rights are important to the Company's
business. The Company's policy is to file patent applications and protect
technology, inventions and improvements to inventions that are commercially
important to the development of its business. The Company also relies on trade
secrets, know-how, continuing technology innovations and licensing opportunities
to develop and maintain its competitive position.
 
     The Company has one issued U.S. patent and 6 pending U.S. patent
applications, all of which have been foreign filed. Two of the patent
applications are co-owned with co-inventors. The Company has one exclusive
worldwide license to a patent, an exclusive license to one U.S. patent and three
worldwide exclusive licenses to patent applications. The Company also has a
non-exclusive license to one U.S. patent. There is no assurance that patents
will issue from these applications or that any patent will issue on technology
arising from additional research or, if patents do issue, that claims allowed
will be sufficient to protect the Company's technology. The patent application
process takes several years and entails considerable expense. In addition, with
respect to each of the Company's co-owned patent applications, the Company has
an option to obtain an exclusive, worldwide, transferable, royalty-bearing
license for such technology, and is currently in discussions with one of the
co-inventors to obtain such a license. In the event the Company is unable to
negotiate exclusive rights to such co-owned technology, each co-inventor may
have rights to independently make, use, offer to sell or sell the patented
technology. Commercialization, assignment or licensing of such technology by a
co-inventor could have a material adverse effect on the Company's business,
financial condition and results of operations. The failure to obtain patent
protection on the Company's technologies or proposed products may have a
material adverse effect on the Company's competitive position and business
prospects.
 
     The patent positions of pharmaceutical and biotechnology firms are
generally uncertain and involve complex legal and factual questions. To date,
there has emerged no consistent policy regarding the breadth of claim allowed in
biotechnology patents. Patent applications in the United States are maintained
in secrecy until a patent issues, and the Company cannot be certain that others
have not filed applications for technology covered by the Company's patent
applications or that the Company was first to file patent applications for such
technology. Competitors may have filed applications for, or may have received
patents and may obtain additional patents and proprietary rights relating to
compounds or processes that block or compete with those of the Company.
 
     There can be no assurance that third parties will not assert patent or
other intellectual property infringement claims against the Company with respect
to its products or technology or other matters. There may be third-party patents
and other intellectual property relevant to the Company's products and
technology which are not known to the Company. A number of the gene sequences or
proteins encoded by certain of those sequences that the Company is investigating
or may use in its products are or may become patented by others. As a result,
the Company may be required to obtain licenses to such gene sequences or other
technology in order to test, use or market products that contain proprietary
gene sequences or encode proprietary proteins. For example, in connection with
its anemia program, the Company anticipates that it may need to obtain a license
to a gene for human erythropoietin. There can be no assurance that the Company
will be able to obtain this or any other license on terms favorable to the
Company, if at all.
 
                                       16
<PAGE>   19
 
     Patent litigation is becoming more widespread in the biotechnology
industry. Litigation may be necessary to defend against or assert claims of
infringement, to enforce patents issued to the Company, to protect trade secrets
owned by the Company, or to determine the scope and validity of proprietary
rights of third parties. Although no third party has asserted that the Company
is infringing such third party's patent rights or other intellectual property,
there can be no assurance that litigation asserting such claims will not be
initiated, that the Company would prevail in any such litigation, or that the
Company would be able to obtain any necessary licenses on reasonable terms, if
at all. Any such claims against the Company, with or without merit, as well as
claims initiated by the Company against third parties, can be time-consuming and
expensive to defend or prosecute and to resolve. If competitors of the Company
prepare and file patent applications in the United States that claim technology
also claimed by the Company, the Company may have to participate in interference
proceedings declared by the Patent and Trademark Office to determine priority of
invention, which could result in substantial cost to the Company, even if the
outcome is favorable to the Company. In addition, to the extent outside
collaborators apply technological information developed independently by them or
by others to the Company's product development programs or apply Avigen's
technologies to other projects, disputes may arise as to the ownership of
proprietary rights to such technologies.
 
     The Company also relies on a combination of trade secret and copyright law,
employee and third-party nondisclosure agreements, and other protective measures
to protect intellectual property rights pertaining to its products and
technology. There can be no assurance, however, that these agreements will
provide meaningful protection of the Company's trade secrets, know-how or other
proprietary information in the event of any unauthorized use, misappropriation
or disclosure of such trade secrets, know-how or other proprietary information.
In addition, the laws of certain foreign countries do not protect the Company's
intellectual property rights to the same extent as do the laws of the United
States. There can be no assurance that the Company will be able to protect its
intellectual property successfully.
 
PRODUCT LIABILITY INSURANCE
 
     The manufacture and sale of medical products entail significant risk of
product liability claims. The Company currently does not carry product liability
insurance, although it intends to obtain such coverage prior to beginning
clinical trials. There can be no assurance that such coverage will be adequate
to protect the Company from any liabilities it might incur in connection with
the sale of the Company's products. In addition, the Company may require
increased product liability coverage as products are commercialized. Such
insurance is expensive and in the future may not be available on acceptable
terms, if at all. A successful product liability claim or series of claims
brought against the Company in excess of its insurance coverage could have a
material adverse effect on the Company's business and results of operations.
 
EMPLOYEES
 
     As of September 21, 1998, the Company had 44 full-time employees, 11 of
whom have Ph.D. or M.D. degrees, including 35 employees in research and
development, and 9 in general administration and finance. The Company also
relies on a number of part-time employees and consultants. None of the Company's
employees is represented by a collective bargaining agreement nor has the
Company ever experienced a work stoppage. The Company believes that its
relationship with its employees is good.
 
SCIENTIFIC ADVISORY BOARD
 
     The Company has established a Scientific Advisory Board, consisting of
experts in the field of medicine, genetics and molecular biology, which reviews
and evaluates the Company's research programs and advises the Company with
respect to technical matters in fields in which the Company is involved. The
members of the Scientific Advisory Board are prominent scholars in their field
and, as a result, may serve as consultants to a wide variety of companies. The
Company's Scientific Advisory Board includes:
 
     Jef D. Boeke, Ph.D., is a professor of Molecular Biology and Genetics at
The Johns Hopkins University School of Medicine. Dr. Boeke co-invented the
capsid targeted viral inactivation technology that provides a basis for Avigen's
antiviral product development program. and has authored more than 100
publications.
 
                                       17
<PAGE>   20
 
     Katherine A. High, M.D., is the William H. Bennett Associate Professor of
Pediatrics at the University of Pennsylvania and the Director of Research of the
Hematology Division at Children's Hospital of Philadelphia. She is an expert in
both the basic science and clinical aspects of hemophilia.
 
     Mark A. Israel, M.D., is Professor of Neurological Surgery and Pediatrics
and Director, the Preuss Laboratory of Molecular Neuro-oncology at the
University of California, San Francisco. Dr. Israel's research focuses on the
molecular and cellular biology of tumors of the nervous system.
 
     Yuichi Iwaki, M.D., Ph.D., is Professor of Urology and Surgery at the
University of Southern California. He also is Director, Transplantation
Immunology and Immunogenetic Laboratory at the University of Southern California
and is a Director of Avigen, Inc.
 
     Y.W. Kan, M.D., D.Sc., is the Louis K. Diamond Professor of Hematology at
the University of California at San Francisco. He also is an Investigator of the
Howard Hughes Medical Institute. Dr. Kan was the 1991 recipient of the Albert
Lasker Clinical Medical Research Award and is noted as a leader in the fields of
sickle cell anemia and thalassemia.
 
     Mark Kay, M.D., Ph.D., is a faculty member at the University of Washington.
Dr. Kay was a recipient of the Upjohn Achievement Award for Excellence in
Clinical Pharmacology and the Henry Christian Award for Excellence in Research.
Dr. Kay was honored recently as an electee to the Board of Directors of the
newly formed American Society of Gene Therapy. Dr. Kay is also a member of the
editorial boards at Gene Therapy and Human Gene Therapy. As of August 1, 1998,
Dr. Kay assumed the position of Director -- Program in Human Gene Therapy, and
Associate Professor -- Department of Pediatrics and Genetics at Stanford
University School of Medicine.
 
     Keiya Ozawa, M.D., Ph.D., is a professor of Molecular Biology, Institute of
Hematology, at Jichi Medical School in Japan, where he has established a
research and preclinical program in gene therapy. Dr. Ozawa is regarded as one
of the leading authorities on gene therapy in Japan and is responsible for
drafting the Japanese government's gene therapy guidelines.
 
     Jeffrey M. Rosen, Ph.D., is a professor of Cell Biology at Baylor College
of Medicine. Dr. Rosen is an internationally recognized expert in the field of
gene expression, and his research focuses primarily on the mechanisms of
tissue-specific gene expression in the mammary and prostate glands.
 
ITEM 2. PROPERTIES
 
THE COMPANY
 
     The Company's facility, located in Alameda, California, is an approximately
23,000 square foot facility leased through May 2003. The Company believes that
it will be able to renew the lease of this facility or find suitable alternate
facilities in the same general area without a material disruption of its
operations. Within the 23,000 square foot facility, the Company completed in
October 1996 of a 7,000 square foot expansion of its research and development
facilities and administration offices.
 
ITEM 3. LEGAL PROCEEDINGS
 
     (a) No material legal proceedings to which Avigen was a party or of which
any of its property was the subject were pending during fiscal 1998.
 
     (b) No material legal proceedings were terminated during fiscal 1998.
 
ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS
 
     None.
 
                                       18
<PAGE>   21
 
                                    PART II
 
ITEM 5. MARKET FOR REGISTRANTS COMMON EQUITY AND RELATED STOCKHOLDER MATTERS
 
     Shares of the Company's common stock commenced trading in the
over-the-counter market on the NASDAQ National Market on May 22, 1996, under the
symbol "AVGN".
 
     The Company has never paid cash dividends and does not anticipate paying
cash dividends in the forseeable future.
 
     The following table sets forth, for fiscal periods indicated, the range of
high and low intraday sale prices available for the fiscal year 1997 and 1998.
 
<TABLE>
<CAPTION>
                           1997                               HIGH      LOW
                           ----                              ------    ------
<S>                                                          <C>       <C>
Year End 6/30/97...........................................  $7.375    $3.25
</TABLE>
 
<TABLE>
<CAPTION>
                           1998                               HIGH      LOW
                           ----                              ------    ------
<S>                                                          <C>       <C>
Year End 6/30/98...........................................    $5      $1.875
</TABLE>
 
     As of September 21, 1998, there were approximately 120 holders of record of
the Company's Common Stock.
 
                                       19
<PAGE>   22
 
ITEM 6. SELECTED FINANCIAL DATA
 
<TABLE>
<CAPTION>
                                            FISCAL YEARS ENDED JUNE 30,
                                  -----------------------------------------------   OCTOBER 22, 1992 (INCEPTION)
                                      1998             1997             1996              TO JUNE 30, 1995
                                  -------------    -------------    -------------   ----------------------------
                                  (IN THOUSANDS, EXCEPT SHARE AND PER SHARE DATA)
<S>                               <C>              <C>              <C>             <C>
STATEMENT OF OPERATIONS DATA:
  Grant revenue.................   $      -0-       $       98       $       87               $   178
  Expenses:
     Research and development...        6,235            4,033            2,550                 5,780
     General and
       administrative...........        2,990            2,351            1,102                 3,155
                                   ----------       ----------       ----------               -------
                                        9,225            6,384            3,652                 8,935
                                   ----------       ----------       ----------               -------
 
  Loss from operations..........       (9,225)          (6,286)          (3,565)               (8,757)
  Interest income (expense)
     (net)......................          365             (710)            (531)                  (40)
  Other income (expense)........          (17)              (2)              (1)                  189
                                   ----------       ----------       ----------               -------
  Net loss......................   $   (8,877)      $   (5,578)      $   (4,097)              $(8,608)
                                   ----------       ----------       ----------               -------
  Net loss per share............   $    (1.22)      $     (.77)
                                   ==========       ==========
  Proforma net loss per share...           --               --       $     (.80)
                                   ----------       ----------       ----------
  Shares used in per share
     calculation................    7,298,271        7,286,146        5,141,951
                                   ==========       ==========       ==========
BALANCE SHEET DATA:
  Cash, cash equivalents and
     investments in marketable
     securities.................   $    4,477       $   13,039       $   16,443               $   203
  Working capital...............        4,635           11,936           15,364                  (916)
  Total assets..................        5,997           14,760           17,532                 1,841
  Capital lease obligations:
     Current....................          587              396               31                     4
     Long-term..................          860            1,084              176                   214
  Deficit accumulated during
     development stage..........      (27,160)         (18,283)         (12,705)               (8,608)
  Stockholders' equity..........        3,583           12,341           16,027                   184
</TABLE>
 
                                       20
<PAGE>   23
 
ITEM 7. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS
 
     This Management's Discussion and Analysis of Financial Condition and
Results of Operations contain forward-looking statements that involve risks and
uncertainties. The Company's actual results may differ significantly from the
results discussed in the forward-looking statements. Factors that might cause or
contribute to such a difference include, but are not limited to, those discussed
herein and in "Risk Factors" in Part I.
 
OVERVIEW
 
     Since its inception, the Company has devoted substantially all of its
resources to research and development activities. The Company is a development
stage company and has not received any revenue from the sale of products. The
Company does not anticipate generating revenue from the sale of products in the
foreseeable future. The Company expects its source of revenue, if any, for the
next several years to consist of government grants and payments under
collaborative arrangements. The Company has incurred losses since its inception
and expects to incur substantial losses over the next several years due to
ongoing and planned research and development efforts, including preclinical
studies and clinical trials. At June 30, 1998 the Company had an accumulated
deficit of $27.2 million.
 
RESULTS OF OPERATIONS
 
  FISCAL YEARS ENDED JUNE 30, 1996, 1997 AND 1998.
 
     Grant revenue increased from $87,000 for the year ended June 30, 1996 to
$98,000 for the year ended June 30, 1997, and decreased to -0- for the year
ended June 30, 1998. Grant revenue for 1996, 1997 and 1998 consisted of
reimbursements under a NIH grant. Revenues earned under research grants are
determined by the timing of the award from the issuing agency. As a result,
research grant revenue earned in one period is not predictive of research grant
revenue to be earned in future periods.
 
     The Company's research and development expenses increased from $2.6 million
for the year ended June 30, 1996 to $4 million for the year ended June 30, 1997,
and increased to $6.2 million for the year ended June 30, 1998. The increase
from fiscal 1996 to fiscal 1997 was due primarily to increases in personnel,
employee related expenses, outside labs, temporary employees and increases in
depreciation expense. The increase from fiscal 1997 to fiscal 1998 was due
primarily to increases in personnel and temporary employees. The Company expects
research and development spending to increase significantly over the next
several years as the Company expands research and product development efforts.
 
     General and administrative expenses increased from 1.1 million for the year
ended June 30, 1996 to 2.4 million for the year ended June 30, 1997 and
increased to 3.0 million for the year ended June 30, 1998. The increase from
fiscal 1996, fiscal 1997 and fiscal 1998 was due primarily to increases in
executive personnel and costs associated with operating as a public company.
General and administrative expenses are expected to increase as the level of the
Company's activities increases but to decrease as a percentage of total
expenses, with the expansion of the research and development efforts.
 
     Interest expense decreased from $581,000 for the year ended June 30, 1996
to $70,000 for the year ended June 30, 1997 and increased to $222,000 for the
year ended June 30, 1998. The decrease from fiscal 1996 to fiscal 1997 was due
primarily to the interest expense incurred related to the Company's bridge
financing for the initial public offering in fiscal year 1996. The increase from
fiscal 1997 to 1998 was due primarily to the Company's utilization of the
equipment lease line.
 
     Interest income increased from $50,000 for the year ended June 30, 1996 to
$780,000 for the year ended June 30, 1997 and decreased to $587,000 for the year
ended June 30, 1998. The increase from fiscal 1996 to fiscal 1997 was due
primarily to the investment of the proceeds of the initial public offering. The
decrease from fiscal 1997 to fiscal 1998 was due primarily to the decreasing
balance of the proceeds of the initial public offering.
 
                                       21
<PAGE>   24
 
LIQUIDITY AND CAPITAL RESOURCES
 
     In May 1996, the Company consummated an initial public offering (the
"Offering") of 2,500,000 shares of Common Stock which raised approximately $17.7
million, net of expenses. In July 1996, the Company issued 250,000 additional
shares of Common Stock in connection with the exercise of the underwriters'
over-allotment option. Net proceeds from such sale were approximately
$1,850,000.
 
     Prior to May 1996, the Company financed its operations primarily through
private placements of Common Stock and Preferred Stock and a bridge financing
which was completed on March 29, 1996 (the "1996 Bridge Financing"). Through
March 31, 1996, the Company had raised approximately $11.0 million, net of
financing costs, from the sale of Common Stock and Preferred Stock and $1.9
million from the 1996 Bridge Financing.
 
     In March 1996, the Company completed the 1996 Bridge Financing in which the
Company issued $1,937,500 principal amount of promissory notes (the "Notes") and
warrants to purchase 193,750 shares of Common Stock. The Notes accrued interest
at the rate of 12% per year and were paid in June 1996 with a portion of the
proceeds from the Company's initial public offering. The warrants expire in
March 2001. The warrants were assigned a value of $300,000. This amount was
reflected as a discount on the Notes and was accreted as additional financing
(interest) expense over the term of the Notes. In connection with the 1996
Bridge Financing, the Company paid the placement agent a commission equal to 10%
of the gross proceeds and warrants to purchase 19,375 shares of Common Stock.
The placement agent warrants expire in May, 2001.
 
     At June 30, 1998, the Company had cash, cash equivalents and investments in
marketable securities of approximately $4.5 million. The Company expects its
cash requirements to increase significantly in future periods. The Company will
require substantial funds to conduct the research and development activities and
preclinical studies and clinical testing of its potential products and to market
any products that are developed. The Company's facility is an approximately
23,000 square foot facility leased through May 2003. The Company believes that
it will be able to renew the lease of this facility and find suitable alternate
facilities in the same general area without a material disruption of its
operations. Within the 23,000 square foot facility, the Company completed in
October 1996 with the commencement of a 7,000 square foot expansion of its
research and development facilities and administration offices. The construction
cost was approximately $500,000. In November 1996, the Company secured a $2
million revolving line of credit with Wells Fargo Bank. In May 1997 the Company
secured a $2 million capital lease from which $1.4 million was used as a
sale-leaseback of existing equipment and for other leasehold improvements. To
the extent the Company decides to develop its own manufacturing facilities, the
Company would require substantial additional capital. The Company's cash
requirements may vary materially from those now planned because of the results
of research, development and clinical trials, the time and costs involved in
obtaining regulatory approvals, the cost of filing, prosecuting, defending and
enforcing patent claims and other intellectual property rights, competing
technological and market developments, changes in the Company's existing
research relationships, the ability of the Company to establish collaborative
arrangements, the development of commercialization activities and arrangements
and the purchase of additional capital equipment.
 
     The Company's common stock is traded on the Nasdaq National Market
("Nasdaq"). In order to maintain its listing on Nasdaq, the Company must
maintain net tangible assets, market capitalization and public float at
specified levels, and generally must maintain a minimum bid price of $1.00 per
share. The Company believes that maintaining its listing on Nasdaq is central to
its ability to raise additional funds as well as to provide liquidity to
investors. The Company failed to meet the Nasdaq net tangible asset listing
requirement at June 30, 1998. The Company will be required to generate
sufficient revenue or raise additional capital to maintain Nasdaq listing
requirements through second fiscal quarter 1999.
 
     The Company believes that the available cash and cash equivalents and
short-term investments, will be sufficient to meet the Company's operating
expenses and capital requirements for at least the next 12 months. The Company
will be required to seek additional funds through public or private financings
or collaborative arrangements with corporate partners. Issuances of additional
equity securities could result in substantial dilution to stockholders. There
can be no assurance that additional funding will be available on terms
                                       22
<PAGE>   25
 
acceptable to the Company, if at all. The failure to fund its capital
requirements would have a material adverse effect on the Company's business.
 
     The Company is aware of the issues associated with the programming code in
existing computer systems as the year 2000 approaches. The "year 2000 problem"
is pervasive and complex as virtually every computer operation will be affected
in some way by the rollover of the two digit year value to 00. The issue is
whether computer systems will properly recognize date-sensitive information when
the year changes to 2000. Systems that do not properly recognize such
information could generate erroneous data or fail. The Company is in the process
of working with its software vendors to ensure that the software that the
Company has licensed from third parties will operate properly in the year 2000
and beyond. In addition, the Company is working with its external suppliers and
service providers to ensure that they and their systems will be able to support
the Company's needs and, where necessary, interoperate with the Company's server
and networking hardware and software infrastructure in preparation for the year
2000. Management does not anticipate that the Company will incur significant
operating expenses or be required to invest heavily in computer systems
improvements to be year 2000 compliant. However, significant uncertainty exists
concerning the potential costs and effects associated with any year 2000
compliance. Any year 2000 compliance problems of either the Company, its
customers or vendors could have a material adverse effect on the Company's
business, results of operations and financial condition.
 
ITEM 8. FINANCIAL STATEMENTS
 
     The financial statements required by this item are set forth beginning at
page F1 of this report.
 
ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND
FINANCIAL DISCLOSURE
 
     None.
 
                                    PART III
 
ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT
 
     The information required is hereby incorporated by reference from the
information contained in the Company's definitive Proxy Statement with respect
to the Company's Annual Meeting of Stockholders, to be held November 19, 1998
(the "Proxy Statement").
 
ITEM 11. EXECUTIVE COMPENSATION
 
     The information required by this item is hereby incorporated by reference
from information contained in the Proxy Statement.
 
ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT
 
     The information required by this item is hereby incorporated by reference
contained in the Proxy Statement.
 
ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS
 
     The information required by this item is hereby incorporated by reference
from information contained in the Proxy Statement.
 
ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8K
 
     (a) The following documents are filed as part of this Report on Form 10-K:
 
        (1) Financial Statements:
 
              Report of Ernst & Young LLP, Independent Auditors
              Balance Sheets
 
                                       23
<PAGE>   26
 
              Statements of Operations
              Statements of Stockholders' Equity
              Statements of Cash Flows
              Notes to Financial Statements
 
        (2) Financial Statements schedules have been omitted from this report
           because the information is provided in the Financial Statements or is
           not applicable.
 
                                       24
<PAGE>   27
 
        (3) Exhibits
 
<TABLE>
<CAPTION>
    EXHIBIT
    NUMBER                             EXHIBITS
    -------                            --------
    <S>      <C>
     3.1*    Amended and Restated Certificate of Incorporation
     3.2*    Restated Bylaws of the Registrant
     4.1*    Specimen Common Stock Certificate
    10.2*    1993 Stock Option Plan
    10.3*    1996 Equity Incentive Plan
    10.4*    Form of Incentive Stock Option Grant
    10.5*    Form of Nonstatutory Stock Option Grant
    10.6*    1996 Non-Employee Director Stock Option Plan
    10.7*    Form of Series C Investors' Rights Agreement
    10.8*    Form of Indemnification Agreement between the Registrant and
             its directors and executive officers
    10.9*    Form of Common Stock Warrant
    10.10*   Form of Series A Preferred Stock Warrant
    10.11*   Form of Series B Preferred Stock Warrant
    10.12*   Form of Series C Preferred Stock Warrant
    10.13*   Form of Series D Preferred Stock Warrant
    10.14*   Form of Series A Preferred Stock Subscription Agreement
    10.15*   Form of Series B Preferred Stock Subscription Agreement
    10.16*   Form of Series C Preferred Stock Subscription Agreement
    10.17*   Form of Unit Purchase Agreement
    10.19*   Form of Bridge Warrant
    10.20*   License Agreement between the Registrant and Research
             Corporation Technologies, Inc., dated May 15, 1992, as
             amended as of March 21, 1996 and April 26, 1996
    10.21*   License Agreement between the Registrant and The Johns
             Hopkins University, dated November 23, 1993, as amended as
             of March 21, 1996
    10.22*   License Agreement between the Registrant and The University
             of Manitoba, dated February 2, 1994
    10.23*   Form of Underwriters' Warrant
    10.24*   Lease Agreement between Registrant and Redding Management,
             Inc., dated September 15, 1992, as amended June 30, 1995
    10.25*   Registration Rights Agreement between the Registrant and
             certain stockholders named therein, dated November 1992
    10.26*   Registration Rights and Transfer Restriction Agreement
             between the Registrant and Research Corporation
             Technologies, Inc., The Indiana University Foundation and
             Arun Srivastava, dated May 15, 1992, as amended October 1992
    10.27*+  Employment Agreement dated August 10, 1992, between the
             Company and John Monahan.
    10.28*+  Employment Agreement dated October 19, 1992, between the
             Company and Wanda deVlaminck
    10.29+   Employment Agreement dated August 14, 1996, between the
             Company and Thomas J. Paulson
    10.30+   Employment Agreement dated October 23, 1996, between the
             Company and Robert M. Maurer
</TABLE>
 
                                       24
<PAGE>   28
 
<TABLE>
<CAPTION>
    EXHIBIT
    NUMBER                             EXHIBITS
    -------                            --------
    <S>      <C>
    10.31+   Employment Agreement dated December 13, 1993, between the
             Company and Gary Kurtzman
    10.32**  Revolving line of credit signed November 22, 1996 with Wells
             Fargo Bank
    10.33**  Equipment lease dated May 22, 1997 with Transamerica
             Business Credit Corporation
    10.34    Form of Common Stock and Warrant Purchase Agreement
    11.1*    Statement re: computation of net loss per share
    23.1     Consent of Ernst & Young LLP, Independent Auditors
    24.1     Power of Attorney (Reference to the signature page herein)
    27.1     Financial Data Schedule
</TABLE>
 
---------------
 * Filed as an exhibit to the Registrant's Registration Statement on Form S-1
   (No. 333-3220) and incorporated herein by reference.
 
 + Management Contract or Compensation Plan.
 
     (b) The Company has filed no reports on Form 8-K.
 
** Filed as an exhibit to the Registrant's Annual Report on Form 10-K (No.
   0-28222) and incorporated herein by reference.
 
                                       25
<PAGE>   29
 
                                   SIGNATURES
 
     Pursuant to the requirements of Section 13 of 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.
 
Dated: September 27, 1998                 AVIGEN, INC.
 
                                          By:
                                            ------------------------------------
                                                    John Monahan, Ph.D.
                                             President, Chief Executive Officer
                                                         and Director
 
                               POWER OF ATTORNEY
 
     KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints John Monahan and Philip J. Whitcome, and
each or any one of them, his true and lawful attorney-in-fact and agent, with
full power of substitution and resubstitution, for him and in his name, place
and stead, in any and all capacities, to sign any and all amendments (including
post-effective amendments) to this Report, and to file the same, with all
exhibits thereto, and other documents in connection therewith, with the
Securities and Exchange Commission, granting unto said attorneys-in-fact and
agents, and each of them, full power and authority to do and perform each and
every act and thing requisite and necessary to be done in connection therewith,
as fully to all intents and purposes as he might or could do in person, hereby
ratifying and confirming all that said attorneys-in-fact and agents, or any of
them, or their or his substitutes or substitute, may lawfully do or cause to be
done by virtue hereof.
 
     PURSUANT TO THE REQUIREMENTS OF 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
                      ---------                                   -----                     ----
<C>                                                    <S>                           <C>
                                                       President, Chief Executive    September 27, 1998
-----------------------------------------------------  Officer and Director
                 John Monahan, Ph.D.                   (Principal Executive
                                                       Officer)
 
                                                       Chief Financial Officer       September 27, 1998
-----------------------------------------------------
                  Thomas J. Paulson
 
                                                       Controller (Principal         September 27, 1998
-----------------------------------------------------  Accounting Officer)
                     Glenn Bauer
 
                                                       Chairman of the Board         September 27, 1998
-----------------------------------------------------
              Philip J. Whitcome, Ph.D.
 
                                                       Director                      September 27, 1998
-----------------------------------------------------
                Zola Horovitz, Ph.D.
 
                                                       Director                      September 27, 1998
-----------------------------------------------------
              Yuichi Iwaki, M.D., Ph.D.
 
                                                       Director                      September 27, 1998
-----------------------------------------------------
                  Richard T. Pratt
</TABLE>
 
                                       26
<PAGE>   30
 
<TABLE>
<CAPTION>
                      SIGNATURE                                   TITLE                     DATE
                      ---------                                   -----                     ----
<C>                                                    <S>                           <C>
                                                       Director                      September 27, 1998
-----------------------------------------------------
            John K.A. Prendergast, Ph.D.
 
                                                       Director                      September 27, 1998
-----------------------------------------------------
             Lindsay A. Rosenwald, M.D.
 
                                                       Director                      September 27, 1998
-----------------------------------------------------
                 Leonard P. Shaykin
 
                        *By:
  ------------------------------------------------
                 John Monahan, Ph.D.
                  Attorney-in-Fact
</TABLE>
 
                                       27
<PAGE>   31
 
                         INDEX TO FINANCIAL STATEMENTS
 
<TABLE>
<CAPTION>
                                                              PAGE
                                                              ----
<S>                                                           <C>
Report of Independent Auditors..............................   29
Balance Sheets at June 30, 1997 and 1996....................   30
Statements of Operations for Years Ended June 30, 1997, 1996
  and 1995..................................................   31
Statements of Stockholders' Equity for Years Ended June 30,
  1997, 1996 and 1995.......................................   32
Statements of Cash Flows for Years Ended June 30, 1997, 1996
  and 1995..................................................   35
Notes to Financial Statements...............................   36
</TABLE>
 
                                       28
<PAGE>   32
 
               REPORT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS
 
The Board of Directors and Stockholders
Avigen, Inc.
 
We have audited the accompanying balance sheets of Avigen, Inc. (a development
stage company) as of June 30, 1998 and 1997 and the related statements of
operations, stockholders' equity and cash flows each of the three years in the
period ended June 30, 1998 and for the period from October 22, 1992 (inception)
through June 30, 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 financial position of Avigen, Inc. at June 30, 1998
and 1997, and the results of its operations and its cash flows for each of the
three years in the period ended June 30, 1998 and for the period from October
22, 1992 (inception) through June 30, 1998, in conformity with generally
accepted accounting principles.
 
Walnut Creek, California
August 13, 1998, except for Note 10, for which the date is
September 24, 1998.
 
                                       29
<PAGE>   33
 
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                                 BALANCE SHEETS
           (IN THOUSANDS, EXCEPT FOR SHARE AND PER SHARE INFORMATION)
 
                                     ASSETS
 
<TABLE>
<CAPTION>
                                                                    JUNE 30,
                                                              --------------------
                                                                1998        1997
                                                              --------    --------
<S>                                                           <C>         <C>
Current assets:
  Cash and cash equivalents.................................  $  1,280    $  3,407
  Investments in marketable securities......................     3,197       9,632
                                                              --------    --------
Total current assets........................................     4,477      13,039
Property and equipment, net.................................     1,359       1,651
Deposits and other assets...................................       161          70
                                                              --------    --------
          Total assets......................................  $  5,997    $ 14,760
                                                              ========    ========
 
LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable..........................................  $    244    $    434
  Accrued compensation and related expenses.................       147         117
  Other accrued liabilities.................................       384         156
  Current portion of capital lease obligations..............       587         396
                                                              --------    --------
Total current liabilities...................................     1,362       1,103
Accrued rent................................................       192         232
Capital lease obligations, less current portion.............       860       1,084
 
Commitments
 
Stockholders' equity:
  Common stock, $.001 par value, 30,000,000 shares
     authorized, 7,305,858 shares issued and outstanding at
     June 30, 1998; 7,288,580 shares issued and outstanding
     at June 30, 1997.......................................         7           7
  Additional paid-in capital................................    30,782      30,704
  Deferred compensation.....................................       (46)        (87)
  Deficit accumulated during the development stage..........   (27,160)    (18,283)
                                                              --------    --------
Total stockholders' equity..................................     3,583      12,341
                                                              --------    --------
          Total liabilities and stockholders' equity........  $  5,997    $ 14,760
                                                              ========    ========
</TABLE>
 
                            See accompanying notes.
                                       30
<PAGE>   34
 
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                            STATEMENTS OF OPERATIONS
           (IN THOUSANDS, EXCEPT FOR SHARE AND PER SHARE INFORMATION)
 
<TABLE>
<CAPTION>
                                                                                     PERIOD FROM
                                                                                   OCTOBER 22, 1992
                                                  YEAR ENDED JUNE 30,                (INCEPTION)
                                         --------------------------------------        THROUGH
                                            1998          1997          1996        JUNE 30, 1998
                                         ----------    ----------    ----------    ----------------
<S>                                      <C>           <C>           <C>           <C>
Grant revenue..........................  $       --    $       98    $       87        $    363
Expenses:
  Research and development.............       6,235         4,033         2,550          18,598
  General and administrative...........       2,990         2,352         1,102           9,599
                                         ----------    ----------    ----------        --------
                                              9,225         6,385         3,652          28,197
                                         ----------    ----------    ----------        --------
 
Loss from operations...................      (9,225)       (6,287)       (3,565)        (27,834)
Interest expense.......................        (222)          (70)         (581)           (952)
Interest income........................         587           780            50           1,457
Other (expense) income.................         (17)           (1)           (1)            169
                                         ----------    ----------    ----------        --------
Net loss...............................  $   (8,877)   $   (5,578)   $   (4,097)       $(27,160)
                                         ==========    ==========    ==========        ========
Historical basic and diluted net loss
  per share............................  $    (1.22)   $     (.77)
                                         ==========    ==========
Pro forma basic and diluted net loss
  per share............................                              $     (.80)
                                                                     ==========
Shares used in historical basic and
  diluted per share calculation........   7,298,271     7,286,146
                                         ==========    ==========
Shares used in pro forma basic and
  diluted per share calculation........                               5,141,951
                                                                     ==========
</TABLE>
 
                            See accompanying notes.
                                       31
<PAGE>   35
 
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                       STATEMENTS OF STOCKHOLDERS' EQUITY
         PERIOD FROM OCTOBER 22, 1992 (INCEPTION) THROUGH JUNE 30, 1998
                  (IN THOUSANDS, EXCEPT FOR SHARE INFORMATION)
<TABLE>
<CAPTION>
                                                                                          CLASS B
                                                                                        CONVERTIBLE
                                             PREFERRED STOCK        COMMON STOCK        COMMON STOCK     ADDITIONAL
                                           -------------------   ------------------   ----------------    PAID-IN       DEFERRED
                                             SHARES     AMOUNT    SHARES     AMOUNT   SHARES    AMOUNT    CAPITAL     COMPENSATION
                                           ----------   ------   ---------   ------   -------   ------   ----------   ------------
<S>                                        <C>          <C>      <C>         <C>      <C>       <C>      <C>          <C>
Balance at October 22, 1992
  (inception)............................          --    $--            --    $--          --    $--      $    --         $--
  Issuance of common stock at $.004 per
    share in November and December
    1992.................................          --     --       896,062      1          --     --            4          --
  Issuance of common stock at $.554 per
    share from January to June 1993 for
    services rendered....................          --     --        20,316     --          --     --           11          --
  Issuance of common stock at $.004 to
    $.222 per share from November 1992 to
    March 1993 for cash..................          --     --     1,003,406      1          --     --           54          --
  Issuance of Class B common stock at
    $.004 per share in December 1992 for
    cash.................................          --     --            --     --      90,293     --            1          --
  Issuance of Series A preferred stock at
    $4.43 per share from March to June
    1993 for cash (net of issuance costs
    of $410,900).........................     678,865      1            --     --          --     --        2,595          --
  Issuance of Series A preferred stock at
    $3.85 per share in March 1993 for
    cancellation of note payable and
    accrued interest.....................      68,991     --            --     --          --     --          266          --
  Issuance of common stock at $.004 per
    share in November 1993 pursuant to
    antidilution rights..................          --     --        22,869     --          --     --            1          --
  Issuance of Series A preferred stock at
    $4.43 per share from July to November
    1993 for cash and receivable (net of
    issuance costs of $187,205)..........     418,284     --            --     --          --     --        1,665          --
  Issuance of Series B preferred stock at
    $5.54 per share in March 1994 for
    cash (net of issuance costs of
    $34,968).............................     128,031     --            --     --          --     --          674          --
  Issuance of Series C preferred stock at
    $4.87 per share from July 1994 to
    June 1995 for cash and receivables
    (net of issuance costs of
    $259,620)............................     739,655      1            --     --          --     --        3,344          --
 
<CAPTION>
                                             DEFICIT
                                           ACCUMULATED
                                           DURING THE        TOTAL
                                           DEVELOPMENT   STOCKHOLDERS'
                                              STAGE         EQUITY
                                           -----------   -------------
<S>                                        <C>           <C>
Balance at October 22, 1992
  (inception)............................   $     --        $    --
  Issuance of common stock at $.004 per
    share in November and December
    1992.................................         --              5
  Issuance of common stock at $.554 per
    share from January to June 1993 for
    services rendered....................         --             11
  Issuance of common stock at $.004 to
    $.222 per share from November 1992 to
    March 1993 for cash..................         --             55
  Issuance of Class B common stock at
    $.004 per share in December 1992 for
    cash.................................         --              1
  Issuance of Series A preferred stock at
    $4.43 per share from March to June
    1993 for cash (net of issuance costs
    of $410,900).........................         --          2,596
  Issuance of Series A preferred stock at
    $3.85 per share in March 1993 for
    cancellation of note payable and
    accrued interest.....................         --            266
  Issuance of common stock at $.004 per
    share in November 1993 pursuant to
    antidilution rights..................         --              1
  Issuance of Series A preferred stock at
    $4.43 per share from July to November
    1993 for cash and receivable (net of
    issuance costs of $187,205)..........         --          1,665
  Issuance of Series B preferred stock at
    $5.54 per share in March 1994 for
    cash (net of issuance costs of
    $34,968).............................         --            674
  Issuance of Series C preferred stock at
    $4.87 per share from July 1994 to
    June 1995 for cash and receivables
    (net of issuance costs of
    $259,620)............................         --          3,345
</TABLE>
 
                                       32
<PAGE>   36
 
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                 STATEMENTS OF STOCKHOLDERS' EQUITY (CONTINUED)
         PERIOD FROM OCTOBER 22, 1992 (INCEPTION) THROUGH JUNE 30, 1998
                  (IN THOUSANDS, EXCEPT FOR SHARE INFORMATION)
<TABLE>
<CAPTION>
                                                                                          CLASS B
                                                                                        CONVERTIBLE
                                             PREFERRED STOCK        COMMON STOCK        COMMON STOCK     ADDITIONAL
                                           -------------------   ------------------   ----------------    PAID-IN       DEFERRED
                                             SHARES     AMOUNT    SHARES     AMOUNT   SHARES    AMOUNT    CAPITAL     COMPENSATION
                                           ----------   ------   ---------   ------   -------   ------   ----------   ------------
<S>                                        <C>          <C>      <C>         <C>      <C>       <C>      <C>          <C>
  Issuance of Series C preferred stock at
    $4.87 per share in June 1995 for
    cancellation of notes payable........      35,500    $--            --    $--          --    $--      $   173         $--
  Net loss from inception to June 30,
    1995.................................          --     --            --     --          --     --           --          --
                                           ----------    ---     ---------    ---     -------    ---      -------         ---
Balance at June 30, 1995.................   2,069,326      2     1,942,653      2      90,293     --        8,788          --
  Issuance of Series C preferred stock at
    $4.87 per share in July 1995 for cash
    (net of issuance costs of $26,000)...      41,042     --            --     --          --     --          174          --
  Issuance of Series D preferred stock at
    $7.09 per share from October 1995 to
    February 1996 for cash (net of
    issuance costs of $25,279)...........     205,351     --            --     --          --     --        1,430          --
  Issuance of Series D preferred stock at
    $7.09 per share in March 1996 in
    settlement of accounts payable.......      22,574     --            --     --          --     --          160          --
  Issuance of common stock at $.004 per
    share in March 1996 pursuant to
    antidilution rights..................          --     --        17,630     --          --     --            1          --
  Issuance of stock options in February
    1996 in settlement of certain accrued
    liabilities..........................          --     --            --     --          --     --          137          --
  Conversion of Class B common stock to
    common stock.........................          --     --       231,304      1     (90,293)    --           (1)         --
  Issuance of warrants to purchase common
    stock in connection with 1996 bridge
    financing in March 1996..............          --     --            --     --          --     --          300          --
  Conversion of preferred stock to common
    stock in May 1996                      (2,338,293)    (2)    2,355,753      2          --     --           (1)         --
  Issuance of common stock at $8.00 per
    share in connection with the May 1996
    initial public offering (net of
    issuance costs of $798,414 and
    underwriting discount of $1,500,000)           --     --     2,500,000      2          --     --       17,699          --
 
<CAPTION>
                                             DEFICIT
                                           ACCUMULATED
                                           DURING THE        TOTAL
                                           DEVELOPMENT   STOCKHOLDERS'
                                              STAGE         EQUITY
                                           -----------   -------------
<S>                                        <C>           <C>
  Issuance of Series C preferred stock at
    $4.87 per share in June 1995 for
    cancellation of notes payable........   $     --        $   173
  Net loss from inception to June 30,
    1995.................................      8,608          8,608
                                            --------        -------
Balance at June 30, 1995.................     (8,608)           184
  Issuance of Series C preferred stock at
    $4.87 per share in July 1995 for cash
    (net of issuance costs of $26,000)...         --            174
  Issuance of Series D preferred stock at
    $7.09 per share from October 1995 to
    February 1996 for cash (net of
    issuance costs of $25,279)...........         --          1,430
  Issuance of Series D preferred stock at
    $7.09 per share in March 1996 in
    settlement of accounts payable.......         --            160
  Issuance of common stock at $.004 per
    share in March 1996 pursuant to
    antidilution rights..................         --              1
  Issuance of stock options in February
    1996 in settlement of certain accrued
    liabilities..........................         --            137
  Conversion of Class B common stock to
    common stock.........................         --             --
  Issuance of warrants to purchase common
    stock in connection with 1996 bridge
    financing in March 1996..............         --            300
  Conversion of preferred stock to common
    stock in May 1996                             --             (1)
  Issuance of common stock at $8.00 per
    share in connection with the May 1996
    initial public offering (net of
    issuance costs of $798,414 and
    underwriting discount of $1,500,000)          --         17,702
</TABLE>
 
                                       33
<PAGE>   37
 
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                 STATEMENTS OF STOCKHOLDERS' EQUITY (CONTINUED)
         PERIOD FROM OCTOBER 22, 1992 (INCEPTION) THROUGH JUNE 30, 1998
                  (IN THOUSANDS, EXCEPT FOR SHARE INFORMATION)
<TABLE>
<CAPTION>
                                                                                          CLASS B
                                                                                        CONVERTIBLE
                                             PREFERRED STOCK        COMMON STOCK        COMMON STOCK     ADDITIONAL
                                           -------------------   ------------------   ----------------    PAID-IN       DEFERRED
                                             SHARES     AMOUNT    SHARES     AMOUNT   SHARES    AMOUNT    CAPITAL     COMPENSATION
                                           ----------   ------   ---------   ------   -------   ------   ----------   ------------
<S>                                        <C>          <C>      <C>         <C>      <C>       <C>      <C>          <C>
  Proceeds from exercise of options in
    June 1996                                      --    $--         6,178    $--          --    $--      $     3        $  --
  Repurchase of common stock                       --     --       (18,325)    --          --     --           (1)          --
  Deferred compensation                            --     --            --     --          --     --          164         (128)
  Net loss                                         --     --            --     --          --     --           --           --
                                           ----------    ---     ---------    ---     -------    ---      -------        -----
Balance at June 30, 1996                           --     --     7,035,193      7          --     --       28,853         (128)
  Issuance of common stock at $8.00 per
    share in July 1996 in connection with
    the exercise of underwriters'
    over-allotment option (net of
    underwriting discount of $150,000)             --     --       250,000     --          --     --        1,850           --
  Proceeds from exercise of options                --     --         3,387     --          --     --            1           --
  Amortization of deferred compensation            --     --            --     --          --     --           --           41
  Net loss                                         --     --            --     --          --     --           --           --
                                           ----------    ---     ---------    ---     -------    ---      -------        -----
Balance at June 30, 1997                           --     --     7,288,580      7          --     --       30,704          (87)
  Proceeds from exercise of options                --     --        17,278     --          --     --           10           --
  Amortization of deferred compensation            --     --            --     --          --     --           --           41
  Options granted for services                     --     --            --     --          --     --           68           --
  Net loss                                         --     --            --     --          --     --           --           --
                                           ----------    ---     ---------    ---     -------    ---      -------        -----
Balance at June 30, 1998                           --    $--     7,305,858    $ 7          --     --      $30,782        $ (46)
                                           ==========    ===     =========    ===     =======    ===      =======        =====
 
<CAPTION>
                                             DEFICIT
                                           ACCUMULATED
                                           DURING THE        TOTAL
                                           DEVELOPMENT   STOCKHOLDERS'
                                              STAGE         EQUITY
                                           -----------   -------------
<S>                                        <C>           <C>
  Proceeds from exercise of options in
    June 1996                               $     --        $     3
  Repurchase of common stock                      --             (1)
  Deferred compensation                           --             35
  Net loss                                    (4,097)        (4,097)
                                            --------        -------
Balance at June 30, 1996                     (12,705)        16,027
  Issuance of common stock at $8.00 per
    share in July 1996 in connection with
    the exercise of underwriters'
    over-allotment option (net of
    underwriting discount of $150,000)            --          1,850
  Proceeds from exercise of options               --              1
  Amortization of deferred compensation           --             41
  Net loss                                    (5,578)        (5,578)
                                            --------        -------
Balance at June 30, 1997                     (18,283)        12,341
  Proceeds from exercise of options               --             10
  Amortization of deferred compensation           --             41
  Options granted for services                    --             68
  Net loss                                    (8,877)        (8,877)
                                            --------        -------
Balance at June 30, 1998                    $(27,160)       $ 3,583
                                            ========        =======
</TABLE>
 
                            See accompanying notes.
 
                                       34
<PAGE>   38
 
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                            STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)
 
<TABLE>
<CAPTION>
                                                                                                  PERIOD FROM
                                                                                                OCTOBER 22, 1992
                                                                   YEAR ENDED JUNE 30,            (INCEPTION)
                                                              ------------------------------        THROUGH
                                                               1998        1997       1996       JUNE 30, 1998
                                                              -------    --------    -------    ----------------
<S>                                                           <C>        <C>         <C>        <C>
OPERATING ACTIVITIES
Net loss....................................................  $(8,877)   $ (5,578)   $(4,097)       $(27,160)
Adjustments to reconcile net loss to net cash used in
  operating activities:
    Depreciation and amortization...........................      678         558        412           2,354
    Amortization of deferred compensation...................       41          41         35             116
    Write-off of organization costs.........................       --          --         --             146
    Noncash interest expense................................       --          --        494             510
    Common stock issued for services........................       --          --         --              11
    Stock options issued for services.......................       68          --         --              68
    Changes in operating assets and liabilities:
       Prepaids, deposits and other assets..................      (91)        (35)        11            (161)
       Accounts payable, other accrued liabilities and
         accrued compensation and related expenses..........       67        (341)        82           1,071
       Accrued rent.........................................      (39)        (17)        75             192
                                                              -------    --------    -------        --------
Net cash used in operating activities.......................   (8,153)     (5,372)    (2,988)        (22,853)
INVESTING ACTIVITIES
Purchases of property and equipment.........................     (387)     (1,156)       (57)         (3,460)
Disposal of property and equipment..........................       --          --         47              47
Organization costs..........................................       --          --         --            (219)
Purchase of marketable securities...........................   (7,405)    (22,514)    (8,352)        (38,270)
Sale of marketable securities...............................   13,840      21,233         --          35,073
                                                              -------    --------    -------        --------
Net cash provided by (used in) investing activities.........    6,048      (2,437)    (8,362)         (6,829)
FINANCING ACTIVITIES
Proceeds from notes payable.................................       --          --        200           2,133
Repayment of notes payable..................................       --          --       (200)         (1,710)
Proceeds from 1996 bridge financing.........................       --          --      1,937           1,937
Payment of bridge financing costs...........................       --          --       (194)           (194)
Repayment of 1996 bridge financing..........................       --          --     (1,937)         (1,937)
Payments on capital lease obligations.......................     (522)       (165)       (11)           (706)
Proceeds from sale-leaseback of equipment...................      490       1,437         --           1,927
Proceeds from issuance of preferred stock, net of issuance
  costs.....................................................       --          --      1,738           9,885
Proceeds from issuance of common stock, net of issuance
  costs and repurchases.....................................       10       1,852     17,705          19,627
                                                              -------    --------    -------        --------
Net cash (used in) provided by financing activities.........      (22)      3,124     19,238          30,962
Net (decrease) increase in cash and cash equivalents........   (2,127)     (4,685)     7,888           1,280
Cash and cash equivalents, beginning of period..............    3,407       8,092        203              --
                                                              -------    --------    -------        --------
Cash and cash equivalents, end of period....................  $ 1,280    $  3,407    $ 8,091        $  1,280
                                                              =======    ========    =======        ========
SUPPLEMENTAL DISCLOSURE
Issuance of preferred stock for cancellation of accounts
  payable, notes payable and accrued interest...............  $    --    $     --    $   160        $    499
Issuance of stock options for repayment of certain accrued
  liabilities...............................................       --          --        137             137
Issuance of warrants in connection with bridge financing....       --          --        300             300
Deferred compensation related to stock option grants........       --          --        163             163
Purchase of property and equipment under capital lease
  financing.................................................       --          --         --             226
Cash paid for interest......................................      222          70         87             459
</TABLE>
 
                                       35
<PAGE>   39
 
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                         NOTES TO FINANCIAL STATEMENTS
 
 1. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES
 
ORGANIZATION, DESCRIPTION OF BUSINESS AND BASIS OF PRESENTATION
 
     Avigen, Inc. (the "Company") was incorporated on October 22, 1992 in
Delaware for the purpose of development and commercialization of gene-based
therapeutic products.
 
     The Company's activities since inception have consisted principally of
acquiring product rights, raising capital, establishing facilities and
performing research and development. Accordingly, the Company is considered to
be in the development stage.
 
     The Company expects to continue to have substantial losses over the next
several years during its development state. The Company plans to meet its
capital requirements primarily through issuances of equity securities, research
and development contract revenue, and in the longer term, revenue from product
sales. The Company intends to seek additional funding through public or private
equity or debt financing, when market conditions allow. There can be no
assurance that the Company will be able to enter into financing arrangements on
acceptable terms or at all. Without such additional funding, the Company may be
required to delay, reduce the scope of or eliminate one or more of its research
or development programs. If the Company cannot raise additional capital,
management will reduce its operations to continue as a going concern through at
least June 30, 1999.
 
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 amounts reported in the financial statements and
accompanying notes. Actual results could differ from those estimates.
 
CASH, CASH EQUIVALENTS, AND MARKETABLE SECURITIES
 
     The Company considers all highly liquid investments with a maturity of
three months or less when purchased to be cash equivalents. The Company accounts
for its marketable securities in accordance with Statement of Financial
Accounting Standards No. 115, "Accounting for Certain Investments in Debt and
Equity Securities." The Company's marketable securities consist principally of
available-for-sale government and corporate debt securities with a minimum
short-term rating of A1/P1 and a minimum long-term rating of A and with
maturities of less than one year. Realized and unrealized gains and losses have
been insignificant to the results of operations and financial position of the
Company. All investments are classified as available for sale. Total cash, cash
equivalents, and marketable securities, at amounts which approximate fair value,
are as follows (in thousands):
 
<TABLE>
<CAPTION>
                                                                 JUNE 30,
                                                             ----------------
                                                              1998      1997
                                                             ------    ------
<S>                                                          <C>       <C>
Cash in banks..............................................  $1,280    $1,477
Corporate debt securities..................................     486     8,361
Federal Home Loan Mortgage Obligations.....................     999        --
U.S. Treasury Notes........................................   1,712     3,201
                                                             ------    ------
                                                             $4,477    $13,039
                                                             ======    ======
</TABLE>
 
RESTRICTED CASH
 
     Deposits and other assets at June 30, 1998 include a $151,000 cash deposit
maintained under the terms of an equipment lease.
 
                                       36
<PAGE>   40
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 1. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (CONTINUED)
PROPERTY AND EQUIPMENT
 
     Property and equipment are stated at cost, less accumulated depreciation.
Depreciation is provided over the estimated useful lives of the respective
assets, which range from five to seven years, using the straight-line method.
 
     Leasehold improvements and assets under capital leases are amortized over
the lives of the related leases or their estimated useful lives, whichever is
shorter, using the straight-line method.
 
RESEARCH AND DEVELOPMENT COSTS
 
     Costs to develop the Company's products are expensed as incurred in
accordance with Statement of Financial Accounting Standards No. 2, "Accounting
for Research and Development Costs," which establishes accounting and reporting
standards for research and development.
 
STOCK-BASED COMPENSATION
 
     The Company has elected to follow Accounting Principles Board Opinion No.
25, "Accounting for Stock Issued to Employees," ("APB 25") and related
interpretations in accounting for its employee stock options because the
alternative fair value accounting provided for under FASB Statement No. 123,
"Accounting for Stock-Based Compensation," ("SFAS 123") requires use of option
valuation models that were developed for use in estimating the fair value of
traded options that have no vesting restrictions and are fully transferable and
not for use in valuing employee stock options. Under APB 25, because the
exercise price of the Company's employee stock options equals the market price
of the underlying stock on the date of grant, no compensation expense is
recognized.
 
BASIC AND DILUTED NET LOSS PER SHARE
 
     In 1997, the Financial Accounting Standards Board issued Statement of
Financial Accounting Standards No. 128 ("SFAS 128"), "Earnings Per Share." SFAS
128 replaced the previously reported primary and fully diluted earnings per
share with basic and diluted earnings per share. Unlike primary earnings per
share, basic earnings per share excludes any dilutive effects of stock options,
warrants, and convertible securities. Basic net loss per share is computed using
the weighted-average number of common shares outstanding. Diluted net loss per
share excludes the effect of the potential shares to be issued upon the assumed
exercise of the options and warrants because the effect of inclusion of such
shares would be antidilutive due to the loss for all periods presented. All net
loss per share amounts for all periods have been presented, and where necessary,
restated to conform to SFAS 128 requirements. The adoption of SFAS 128 did not
have a material impact on the Company's earnings per share calculation for all
periods presented.
 
     Pro forma net loss per share, as presented in the accompanying statements
of operations, has been computed as described above and also gives effect to
common equivalent shares from convertible preferred stock issued from the
initial public offering that automatically converted upon completion of the
Company's initial public offering (using the if-converted method) from the
original date of issuance.
 
RECENT ACCOUNTING PRONOUNCEMENTS
 
     Effective July 1, 1998, the Company will be required to adopt Financial
Accounting Standards Board's Statement of Financial Accounting Standard No. 130
("SFAS 130"), "Reporting Comprehensive Income." SFAS 130 establishes new rules
for the reporting and display of comprehensive income and its components;
 
                                       37
<PAGE>   41
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 1. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (CONTINUED)
however, the adoption of this statement is not expected to have a significant
impact on the Company's financial position or results of operations.
 
     Effective for the financial statements for the year ended June 30, 1999,
the Company will be required to adopt Financial Accounting Standards Board's
Statement of Financial Accounting Standard No. 131 ("SFAS 131"), "Disclosures
about Segments of an Enterprise and Related Information." SFAS 131 supersedes
Statement 14, "Financial Reporting for Segments of a Business Enterprise." SFAS
131 establishes standards for the way that public business enterprises report
selected information about operating segments in interim financial reports. SFAS
131 also establishes standards for related disclosures about products and
services, geographic areas and major customers. Given that the Company operates
in one segment, the adoption of SFAS 131 is expected to have no significant
impact on the Company's results of operations, financial position or disclosure
of segment information.
 
 2. LICENSING AGREEMENTS
 
     The Company has entered into various license agreements with universities
and medical research centers for the use of certain technologies related to its
gene therapy product development programs. Generally, such agreements require
the Company to pay the licensor a royalty on sales of products incorporating the
licensed technology. Certain of these agreements require the Company to pay
minimum royalties for specified periods and payments upon the achievement of
specified milestones. These agreements are generally cancelable by the Company
upon written notice without significant financial penalty, or by the licensor if
the Company does not meet development milestones specified in the agreements.
 
     Certain of these license agreements provide for the achievement of
development milestones at various times beginning in February 1997. In the event
the Company fails to achieve such milestones or to obtain extensions, certain of
the license agreements may be terminated by the licensor with relatively short
notice to the Company. Termination of any of the Company's license agreements
could have a material adverse effect on the Company's business.
 
     The Company entered into an exclusive license agreement for the use of
patented technology with Research Corporation Technology ("RCT"). This agreement
requires the Company to achieve certain development milestones in order to
continue to use the technology. The Company must exercise its best efforts to
commercially develop, promote and sell products covered by the licensed patent
rights, and is obligated to file an Investigational New Drug application
("IND"), by the end of 1998 and a product license application or a new drug
application by the end of 2000. In the event the Company fails to achieve any of
these milestones by their applicable deadlines, the Company has the right to pay
RCT additional fees of up to $250,000 to extend certain of the deadlines for
specified periods. RCT may terminate the agreement if the Company becomes
insolvent or bankrupt or fails to perform any of its obligations under the
agreement.
 
 3. NOTES PAYABLE
 
     In March 1996, the Company completed a bridge financing pursuant to which
it issued $1,938,000 principal amount of bridge notes payable including $295,000
to certain stockholders and members of the Board of Directors and warrants to
purchase 193,750 shares of common stock (see Note 5). The bridge notes were
paid, together with interest at the rate of 12% per annum, following the
completion of the Company's May 1996 initial public offering.
 
                                       38
<PAGE>   42
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 4. COMMITMENTS
 
LEASES
 
     The Company leases its facility under a noncancelable operating lease
agreement. The lease agreement has variable payment terms; however, the Company
is recognizing rent expense on a straight-line basis over the life of the lease
which expires in May 2003. The Company has also entered into various capital
leases for property and equipment. The Company secured a $2 million capital
lease facility of which approximately $1.4 million was used by the Company in
fiscal 1997 to complete a sale-leaseback transaction for a portion of its
property and equipment. In fiscal 1998, approximately $490,000 of this lease
facility was used to finance equipment under an additional sale-leaseback
transaction. At June 30, 1998, approximately $110,000 is available under this
facility for future equipment financings. The property and equipment financed
under the sale-leaseback transactions were sold at net book value; therefore, no
gain or loss was realized from these transactions. At June 30, 1998, the Company
also has $3 million available under capital lease facilities for future property
and equipment financings. Future minimum lease payments under noncancelable
operating and capital leases having terms in excess of one year are as follows
(in thousands):
 
<TABLE>
<CAPTION>
                                                           CAPITAL    OPERATING
                                                           LEASES       LEASE
                                                           -------    ---------
<S>                                                        <C>        <C>
Year ending June 30:
  1999...................................................  $  752      $  420
  2000...................................................     828         420
  2001...................................................     119         420
  2002...................................................      --         420
  2003...................................................      --         367
  Thereafter.............................................      --          --
                                                           ------      ------
  Total minimum lease payments...........................   1,699      $2,045
                                                                       ======
  Less amount representing interest......................    (251)
                                                           ------
  Present value of minimum lease payments................   1,447
  Less current portion of capital lease obligations......    (587)
                                                           ------
  Long-term capital lease obligations....................  $  860
                                                           ======
</TABLE>
 
     Rent expense for fiscal 1998 was $425,000 ($398,000 in 1997 and $377,000 in
1996).
 
LINE OF CREDIT
 
     The Company has a $2 million revolving line of credit with a financial
institution that bears interest at the bank's prime rate. As of June 30, 1998,
no amounts have been drawn from these available funds. This line of credit
expires on September 30, 1998 and is collateralized by cash and investments.
 
 5. STOCKHOLDERS' EQUITY
 
COMMON STOCK
 
     In May 1996, the Company consummated an initial public offering of
2,500,000 shares of common stock which raised approximately $17.7 million in
cash, net of expenses.
 
     In May 1996, in contemplation of the initial public offering, the Company
filed an Amended and Restated Certificate of Incorporation to effect a one for
4.43 reverse stock split of all outstanding shares of common stock, preferred
stock, stock options and warrants. All shares and per share data in the
accompanying financial statements have been adjusted retroactively to give
effect to the reverse stock split. The Amended
 
                                       39
<PAGE>   43
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 5. STOCKHOLDERS' EQUITY (CONTINUED)
and Restated Certificate of Incorporation also reduced the authorized stock of
the Company such that the Company is authorized to issue 5,000,000 shares of
preferred stock, and 30,000,000 shares of common stock.
 
WARRANTS
 
     At June 30, 1998, the Company had outstanding warrants to purchase shares
of common stock as follows (see Note 7 for a description of warrants issued to
related parties):
 
<TABLE>
<CAPTION>
SHARES   EXERCISE PRICE          EXPIRATION DATE
------   --------------          ---------------
<S>      <C>              <C>
 61,014  $4.87            November 1998
 78,065  $5.36            June 2000 - September 2005
 14,548  $6.11            March 1999
193,750  $6.40            March 2001
 19,375  $7.04            March 2001
  4,513  $7.09            November 2005
 45,272  $7.80            March 2001
250,000  $9.60            May 2001
-------                   -----------------------------
666,537  $4.87 - 9.60     November 1998 - November 2005
=======                   =============================
</TABLE>
 
     The warrants to acquire 193,750 shares of common stock at an exercise price
of $6.40 were when issued in connection with a bridge financing transaction
("the bridge warrants") in March 1996. The bridge warrants were assigned a value
of $300,000 which was reflected as a discount on the bridge notes and was
accreted as additional financing (interest) expense over the term of the bridge
notes. Management has determined that the fair value of all other warrants is
not material.
 
STOCK OPTION PLANS
 
     In October 1993, the Company established a Stock Option Plan (the "1993
Plan") under which incentive and nonqualified stock options may be granted to
key employees, directors and consultants of the Company to purchase up to
338,600 shares of common stock. Under the 1993 Plan, options may be granted at a
price per share not less than the fair market value at the date of grant as
determined by the Board of Directors. In May 1996, the 1993 Plan was superseded
by the 1996 Stock Option Plan.
 
                                       40
<PAGE>   44
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 5. STOCKHOLDERS' EQUITY (CONTINUED)
     In May 1996, the Company established a Stock Option Plan ("1996 Plan")
which provides for grants of options to employees, directors and consultants of
the Company to purchase up to 1,300,000 shares of common stock. Under the 1996
Plan, options may be granted at a price per share not less than the fair market
value at the date of grant. Options granted generally have a maximum term of 10
years from the grant date and become exercisable over four years. Option
activity under the 1993 and 1996 Plans was as follows:
 
<TABLE>
<CAPTION>
                                                     OUTSTANDING OPTIONS
                                         -------------------------------------------
                                                                         WEIGHTED
                                                                         AVERAGE
                                                    EXERCISE PRICE    EXERCISE PRICE
                                         SHARES         RANGE           PER SHARE
                                         -------    --------------    --------------
<S>                                      <C>        <C>               <C>
Outstanding at June 30, 1994...........   63,204    $ .44                 $ .44
  Granted..............................  115,237    .44 -  .66              .44
  Canceled.............................  (16,930)   .44                     .44
                                         -------
Outstanding at June 30, 1995...........  161,511    .44 -  .66              .44
  Granted..............................  193,476    .44 -  .71              .53
  Canceled.............................  (65,611)   .44 -  .66              .46
  Exercised............................   (6,178)   .44 -  .49              .46
                                         -------
Outstanding at June 30, 1996...........  283,198    .44 -  .71              .52
  Granted..............................  551,127    3.63 - 4.00            3.86
  Canceled.............................   (4,066)   .44 - 3.38              .94
  Exercised............................   (3,387)   .44 -  .71              .50
                                         -------
Outstanding at June 30, 1997...........  826,872    .44 - 4.00             1.94
  Granted..............................  234,025    2.13 - 3.88            2.84
  Canceled.............................  (74,456)   .44 - 3.88             3.23
  Exercised............................  (17,278)   .44 -  .71              .60
                                         -------     ------------         -----
Outstanding at June 30, 1998...........  969,163    $ .44 - 4.00          $2.05
                                         =======     ============         =====
</TABLE>
 
     In July 1995, the Company granted a member of its Board of Directors an
option to purchase 515,248 shares of common stock at $0.49 per share,
exercisable for five years from the date of grant. The shares vest in equal
monthly installments over 36 months. The shares issuable upon exercise of such
options may be issued prior to vesting but such shares are subject to repurchase
at the original price per share upon termination of services to the Company.
Such grant was made outside of the 1993 and 1996 Plans.
 
     In March 1996, the Board of Directors adopted and in April 1996 the
stockholders approved the 1996 Equity Incentive Plan (the "Incentive Plan") and
reserved 600,000 shares of common stock for issuance thereunder. The Incentive
Plan provides for grants of incentive stock options to employees and
nonstatutory stock options, restricted stock purchase awards, stock bonuses and
stock appreciation rights to employees and consultants of the Company. No
options, restricted stock awards, stock bonuses or stock appreciation rights
have been granted under the Incentive Plan.
 
     In March 1996, the Board of Directors adopted and in April 1996 the
stockholders approved the 1996 Non-Employee Directors' Stock Option Plan (the
"Directors' Plan") and reserved 200,000 shares of common stock for issuance
there under. The Directors' Plan provides for automatic grants of options to
purchase shares of common stock to non-employee directors of the Company. The
Directors' Plan was effective upon the closing of the initial public offering.
As of June 30, 1998, options to purchase 70,000 shares of common stock
 
                                       41
<PAGE>   45
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 5. STOCKHOLDERS' EQUITY (CONTINUED)
at $3.25 - $6.00 per share, exercisable for five years from the date of grant,
have been granted under the Directors' Plan. None of the options granted under
the Directors' Plan have been exercised at June 30, 1998.
 
     The following table summarizes information with regard to stock options
outstanding at June 30, 1998:
 
<TABLE>
<CAPTION>
                                OPTIONS OUTSTANDING                    OPTIONS EXERCISABLE
                  -----------------------------------------------   --------------------------
                              WEIGHTED AVERAGE   WEIGHTED AVERAGE             WEIGHTED AVERAGE
   RANGE OF                      REMAINING           EXERCISE                     EXERCISE
EXERCISE PRICES    SHARES     CONTRACTUAL LIFE        PRICE         SHARES         PRICE
---------------   ---------   ----------------   ----------------   -------   ----------------
<S>               <C>         <C>                <C>                <C>       <C>
  $.44 -  .71       764,416         6.94              $ .50         701,572        $ .50
  2.13 - 3.50       274,400         9.37               2.89          39,435         2.92
  3.63 - 3.88       316,595         8.34               3.64         125,492         3.63
  4.00 - 6.00       199,000         8.39               4.35          73,049         4.32
                  ---------                                         -------
                  1,554,411                                         939,548
                  =========                                         =======
</TABLE>
 
     At June 30, 1998, 580,005, 600,000 and 130,000 options were available for
future grant under the 1996 Plan, the Incentive Plan and the Director Plan,
respectively.
 
     The fair value of each option grant is estimated on the date of grant using
the Black-Scholes option pricing model with the following assumptions:
 
<TABLE>
<CAPTION>
                                                           YEAR ENDED JUNE 30,
                                                           --------------------
                                                            1998         1997
                                                           -------      -------
<S>                                                        <C>          <C>
Expected volatility......................................  3.3917       .8448
Risk free interest rate..................................  5.51%        6.44%
Life of options in years.................................  5            5
Expected dividend yield..................................  --           --
</TABLE>
 
     The weighted-average grant-date fair value of options granted during fiscal
1998 and 1997 was $2.75 and $2.78, respectively.
 
     If the Company had elected to recognize compensation cost based on the fair
value of the options granted at grant date as prescribed by SFAS 123, net loss
per share would have been increased to the pro forma amounts indicated in the
table below (in thousands except per share amounts):
 
<TABLE>
<CAPTION>
                                                           YEAR ENDED JUNE 30
                                                           ------------------
                                                            1998       1997
                                                           -------    -------
<S>                                                        <C>        <C>
Net loss -- as reported                                    $(8,876)   $(5,578)
Net loss -- pro forma                                       (9,460)    (5,936)
Net loss per share basic and diluted -- as reported          (1.22)      (.77)
Net loss per share basic and diluted -- pro forma            (1.30)      (.81)
</TABLE>
 
     Because SFAS 123 is applicable only to options granted subsequent to June
30, 1995, the resulting pro forma compensation cost may not be representative of
that expected in future years.
 
     For certain options granted during fiscal 1996, the Company recognized as
deferred compensation the excess of the deemed value for financial reporting
purposes of the common stock issuable upon the exercise of such options over the
aggregate exercise price of such options. Total deferred compensation of
$163,000 is being amortized by changes to operations over the vesting period for
such options.
 
                                       42
<PAGE>   46
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 5. STOCKHOLDERS' EQUITY (CONTINUED)
EMPLOYEE STOCK PURCHASE PLAN
 
     In September 1997, the Company adopted the 1997 Employee Stock Purchase
Plan ("Purchase Plan"). A total of 360,000 shares of common stock have been
reserved for issuance under the Purchase Plan. As of June 30, 1998, there have
been no employee contributions to the Purchase Plan.
 
 6. BALANCE SHEET DETAIL
 
     Accrued liabilities consist of the following (in thousands):
 
<TABLE>
<CAPTION>
                                                                JUNE 30
                                                              ------------
                                                              1998    1997
                                                              ----    ----
<S>                                                           <C>     <C>
Accrued consulting fees.....................................  $157    $ 75
Accrued license fees........................................    98      75
Other.......................................................   129       6
                                                              ----    ----
                                                              $384    $156
                                                              ====    ====
</TABLE>
 
     Property and equipment consist of the following (in thousands):
 
<TABLE>
<CAPTION>
                                                                JUNE 30
                                                           ------------------
                                                            1998       1997
                                                           -------    -------
<S>                                                        <C>        <C>
Leasehold improvements...................................  $ 1,116    $ 1,116
Leasehold improvements under capital lease...............      485        485
Office equipment under capital lease.....................      145        127
Furniture under capital lease............................      154        143
Laboratory equipment under capital lease.................    1,736      1,379
                                                           -------    -------
Property and equipment...................................    3,635      3,249
Accumulated depreciation and amortization................   (2,276)    (1,598)
                                                           -------    -------
Net property and equipment...............................  $ 1,359    $ 1,651
                                                           =======    =======
</TABLE>
 
     Accumulated amortization of assets under capital leases was $1,200,000 and
$745,000 at June 30, 1998 and 1997, respectively.
 
 7. RELATED PARTY TRANSACTIONS
 
     As part of its continuous program of research an development, the Company
retains consultants to advise the Company. Certain of the consultants are
holders of the Company's common stock or options to purchase common stock.
Consulting expenses relating to these stockholders and option holders were
$141,000, $174,000, and $275,000, for fiscal 1998, 1997 and 1996, respectively.
The amounts payable to these consultants at June 30, 1998 and 1997 were
$157,000, and $75,000, respectively.
 
     In fiscal 1998, the Company paid a Board member $100,000 for consulting
services related to services performed for the Company.
 
     A stockholder and Director of the Company (the "Director") is an officer
and sole stockholder of the Placement Agent. In connection with various
preferred stock offerings, the Placement Agent received commissions and expense
reimbursements of $815,000, and warrants to purchase up to 91,415 shares of the
Company's common stock at exercise prices ranging from $4.87 to $7.04 (see Note
5).
 
                                       43
<PAGE>   47
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 7. RELATED PARTY TRANSACTIONS (CONTINUED)
     During fiscal 1996, entities managed by the Director and another member of
the Board of Directors loaned the Company $200,000 which was repaid in December
31, 1996. In connection with these agreements, the Company issued warrants to
purchase 4,513 shares of its common stock with an exercise price of $7.09 per
share (see Note 5).
 
     The Director has personally guaranteed the Company's lease on the office
and laboratory facilities (see Note 4).
 
     The Company has entered into non-exclusive agreements with Maxzen Medical
Technologies ("Maxzen") for the purpose of identifying potential investors in
Japan. The Director of the Company is affiliated with Maxzen. Under the terms of
the agreements, Maxzen receives commissions, payable in cash and warrants, based
on investments in the Company initiated by Maxzen. Through June 30, 1998, Maxzen
has earned commissions under the agreements amounting to $299,000 and warrants
for the purchase of 172,682 shares of common stock at prices ranging from $4.87
to $7.80 (see Note 5).
 
 8. INCOME TAXES
 
     Significant components of the Company's deferred tax assets are as follows
(in thousands):
 
<TABLE>
<CAPTION>
                                                                JUNE 30
                                                          -------------------
                                                            1998       1997
                                                          --------    -------
<S>                                                       <C>         <C>
Net operating loss carryforward                           $  8,664    $ 5,762
Research and development credit carryforwards                  992        621
Depreciation                                                   546        231
Capitalized research and development                         1,048        674
Other                                                          133        141
                                                          --------    -------
Gross deferred tax assets                                   11,388      7,429
Valuation allowance                                        (11,388)    (7,429)
                                                          --------    -------
Net deferred tax assets                                   $     --    $    --
                                                          ========    =======
</TABLE>
 
     Due to the Company's history of losses, a valuation allowance has been
provided against the full amount of deferred tax assets.
 
     The valuation allowance increased by $3,959,000, $2,258,000, and $1,501,000
for fiscal 1998, 1997, and 1996, respectively.
 
     At June 30, 1998, the Company has net operating loss carryforwards for
federal and state income tax purposes of approximately $24,400,000 and
$6,144,000, respectively, which expire in fiscal years ended June 30, 1999
through June 30, 2013. At June 30, 1998, the Company has research and
development credit carryforwards for federal tax purposes of approximately
$746,000, which expire in fiscal years ended June 30, 2009 through June 30,
2013.
 
     Because of the "change in ownership" provisions of the Internal Revenue
Code of 1986, utilization of the Company's tax net operating loss carryforwards
and tax credit carryforwards may be subject to an annual limitation in future
periods. As a result of the annual limitation, a portion of these carryforwards
may expire before ultimately becoming available to reduce future income tax
liabilities.
 
                                       44
<PAGE>   48
                                  AVIGEN, INC.
                         (A DEVELOPMENT STAGE COMPANY)
 
                   NOTES TO FINANCIAL STATEMENTS (CONTINUED)
 
 9. EMPLOYEE PROFIT SHARING/401(k) PLAN
 
     In January 1996, the Company adopted a Tax Deferred Savings Plan under
Section 401(k) of the Internal Revenue Code (the "Plan") for all full-time
employees. Eligible employees can contribute amounts to the Plan via payroll
withholding, subject to certain limitations. The Company's contributions to the
Plan are discretionary. The Company has made no contributions to the Plan
through June 30, 1998.
 
10. SUBSEQUENT EVENT
 
     In August and September 1998, the Company issued 1,196,615 shares of common
stock in a private placement which resulted in cash proceeds of approximately
$2.7 million. The Company also issued warrants to these investors to acquire
239,323 shares at an exercise price ranging from $2.18 to $3.67 per share. The
warrants expire in August and September 2003.
 
                                       45