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UNITED STATESSECURITIES AND EXCHANGE COMMISSIONWashington, D.C.
20549

___________________FORM 10-K/A

Amendment No. 1___________________

(Mark One)



|x | **ANNUAL REPORT
      PURSUANT TO SECTION 13 OR 15(d) OF THE****SECURITIES EXCHANGE ACT OF
  1934**
|- | ---------------------------------------------------------------------------------------------------

For the fiscal year ended December
31, 2008

OR

|o | **TRANSITION
      REPORT PURSUANT TO SECTION 13 OR 15(d) OF THESECURITIES 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)

|Delaware                              | 13-3647113            
|------------------------------------- | ----------------------
|(State or
      other jurisdiction of | (I.R.S.
      Employer
|incorporation or organization)        | Identification No.)   

1301 Harbor Bay ParkwayAlameda,
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:
|-----------------------------------------------------------------
|Title of
      each class                                        
|Common
      Stock, $0.001 par value per share                   

Securities registered pursuant to
Section 12(g) of the Act:

Preferred Share Purchase
Rights(Title of class)

---

Indicate by
check mark if the registrant is a well-known seasoned issuer, as defined in Rule
405 of the Securities Act. Yes o No x

Indicate by check mark if the
registrant is not required to file reports pursuant to Section 13 or Section
15(d) of the Act. Yes o No x

Indicate by check mark whether the
registrant (1) has filed all reports required to be filed by Section 13 or 15(d)
of the Securities Exchange Act of 1934 during the preceding 12 months (or for
such shorter period that the registrant was required to file such reports), and
(2) has been subject to such filing requirements for the past 90 days. Yes x No o

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

Indicate by check mark whether the
registrant is a large accelerated filer, an accelerated filer, a non-accelerated
filer or a smaller reporting company. See the definitions of large accelerated
filer accelerated filer and smaller reporting company in Rule 12b-2 of the
Exchange Act.

| | Large
      accelerated filero                      | Accelerated
      filer x       
| | --------------------------------------------------- | --------------------------------
| |                                                    
| | Non-accelerated
      filero                        | Smaller
      reporting companyo
| | (Do
      not check if a smaller reporting company)

Indicate by
check mark whether the registrant is a shell company (as defined in Rule 12b-2
of the Act). YesoNox

The aggregate market value of the
Common Stock held by non-affiliates of the registrant as of June 30, 2008, was
approximately $85,900,000 based upon the closing sale price of the registrants
Common Stock as reported on the NASDAQ Global Market on such date. Shares of
common stock held by each officer and director have been excluded in that such
persons may be deemed to be affiliates of the registrant. Shares held by all
other stockholders have not been excluded, as no other stockholder held a
percentage of the registrants outstanding Common Stock that the registrant
believes is necessary to exercise control over the registrant, nor has any other
stockholder otherwise exhibited any ability to exercise control over the
registrant.

The number
of outstanding shares of the registrants Common Stock as of March 6, 2009, was
29,769,115 shares.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of
the registrants definitive Proxy Statement for the Special Meeting of
Stockholders filed with the Securities and Exchange Commission pursuant to
Regulation 14A on March 9, 2009, are incorporated by reference in Part III,
Items 10-14 of this Form 10-K.

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EXPLANATORY NOTE

We are filing this amendment to our Annual
Report on Form 10-K, originally filed with the Securities and Exchange
Commission on March 16, 2009, solely for the purpose of amending and
supplementing Part III of the Annual Report on Form 10-K. This amendment changes
our Annual Report only by including information required by Part III (Items 10,
11, 12, 13 and 14). In addition, we are also including Exhibits 31.1 and 31.2
required by the filing of this amendment.

PART III

Item 10.Directors, Executive Officers and Corporate Governance

The information required by this
Item with respect to Executive Officers as of April 28, 2009 is as follows:

|Name                |  | Age |  | Position                                                            
|------------------- |  | --- |  | --------------------------------------------------------------------
|Andrew A. Sauter    |  | 42  |  | President, Chief Executive Officer and Chief Financial
      Officer
|Kirk Johnson, Ph.D. |  | 49  |  | Vice President, Research and Development                            

All of our
officers are elected annually by the Board of Directors. There is no family
relationship between or among any of the officers or directors.

Andrew A.
Sauterwas appointed our Chief Executive
Officer and President in March 2009, and as our Chief Financial Officer in
February 2008 after having served as Vice President, Finance since January 2006.
Mr. Sauter joined Avigen as Controller in November 1999. Mr. Sauter oversees the
entire operations of the company, including the proposed dissolution of the
company and sale of Avigens assets, as well as the financial reporting
obligations of Avigen and its information technology needs. From 1992 to 1999,
Mr. Sauter worked for BankAmerica Corporation in a variety of positions,
including most recently as a vice president in the Capital Markets Finance
organization. From 1989 to 1992, he worked for Ernst & Young LLP. Mr. Sauter
is a certified public accountant and holds a B.A. degree in economics from
Claremont McKenna College.

Kirk
Johnson, Ph.D.,was appointed Vice President,
Research and Development in December 2006, and Secretary in March 2009. Dr.
Johnson joined Avigen in January 2004 and was appointed Vice President,
Preclinical Development in June 2004. Prior to joining Avigen, Dr. Johnson was
Senior Director, Pharmacology & Preclinical Development and a member of the
executive management team of Genesoft Pharmaceuticals, a pharmaceutical company,
from 2001 to 2004. From 1991 to 2001, Dr. Johnson was employed in both protein
and small molecule therapeutic research and development at Chiron Corporation, a
biopharmaceutical company, and eventually served as Director, Pharmacology and
Preclinical Research. Dr. Johnson was involved in leading IND-enabling programs,
supporting clinical development, and contributing to successful IND and NDA
filings at Chiron and Genesoft. In addition to general pharmacology and other
preclinical development responsibilities, he has led research and clinical
development projects for diverse indications including neuropathic pain,
hemophilia, antibacterials, diabetes, obesity, acute inflammation and
cardiovascular disease and has published more than 50 manuscripts and holds 4
U.S. patents. Dr. Johnson earned a B.S. in toxicology from U.C. Davis, and a
Ph.D. in pharmacology and toxicology from the Medical College of Virginia. He
completed postdoctoral fellowships studying the mechanism of action of IL-2 from
1986-1989 with Dr. Kendall Smith at Dartmouth College and from 1990-1991 with
Dr. Marian Koshland at the University of California, Berkeley.

The
information required by this Item with respect to Directors, including
information with respect to our audit committee, audit committee financial
experts and procedures for Board nominations, is incorporated herein by
reference from the information under the captions, Current Directors of Avigen,
Inc. and Information Regarding the Board of Directors and Corporate
Governance appearing in the definitive Proxy Statement delivered to Avigens
stockholders in connection with the solicitation of proxies for Avigens Special
Meeting of Stockholders (the Proxy Statement).

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*Section 16(a) Beneficial
Ownership Reporting Compliance*

The
information required by this Item with respect to compliance with Section 16(a)
of the Exchange Act is incorporated herein by reference from the section
captioned Section 16(a) Beneficial Ownership Reporting Compliance contained in
the Proxy Statement.

*Code of Business Conduct and
Ethics*

The
information required by this Item with respect to our code of ethics is
incorporated herein by reference from the section captioned  Information
Regarding the Board of Directors and Corporate Governance  Code of Business
Conduct and Ethics contained in the Proxy Statement.

Item 11.Executive Compensation

The
information required by this Item, except for the Compensation Committee Report,
Compensation Discussion and Analysis, and Summary Compensation Table, each of
which is set forth below, is set forth in the Proxy Statement under the
captions, Executive Compensation, Compensation Committee, Compensation
Committee Processes and Procedures and Compensation Committee Interlocks and
Insider Participation. Such information is incorporated herein by reference.

Compensation Committee
Report1

The
Compensation Committee has reviewed and discussed with management the
Compensation Discussion and Analysis contained in this Annual Report on Form
10-K/A for the fiscal year ended 2008. Based on this review and discussion, the
Compensation Committee has recommended to the Board of Directors that the
Compensation Discussion and Analysis be included in this Annual Report on Form
10-K/A for the fiscal year ended 2008.

COMPENSATIONCOMMITTEE

JOHNK.A.PRENDERGAST,PH.D.(CHAIR)RICHARDWALLACE,B.COMM.(HONS)STEPHENDILLY,M.B.B.S.,PH.D.

COMPENSATIONDISCUSSIONANDANALYSIS

Compensation Philosophy

Our
compensation approach is designed to reward the achievement of corporate
objectives and individual performances that contribute toward building a
sustainable business that develops differentiated products to improve the health
and quality of life of patients and creates value for our stockholders. To this
end, the Board of Directors and management establish annual and long-term
corporate goals that reflect the priorities of our product and business
development plans. Our Board of Directors and management review these goals on a
regular basis and our Compensation Committee (the Committee) uses these
objectives to determine levels of compensation for executive officers to ensure
management incentives are aligned with the interests of stockholders.

Avigens
compensation practice is designed to provide remuneration packages that are
commensurate with the marketplace in which we compete to attract and motivate
our executive officers, management and staff to achieve our strategic
objectives. Specifically, we review base salaries annually and, along with a
comprehensive array of medical, health, life insurance and disability plans
generally available to all our employees, set salaries at levels that are
intended to attract, engage and retain executive officers whose abilities are
critical to our long-term success and competitiveness. We vary bonus payments
annually based on a performance structure designed to reward results and balance
individual accountability with team-oriented collaboration that fosters
integrity and a high-performance culture. Historically, we also issue
equity-based compensation annually in varying amounts that are intended to
represent a significant portion of each executives total compensation package
because we believe it promotes innovation and calculated assessment and
management of risk designed to achieve Avigens long-term objectives.

____________________1The
material in this report is not soliciting material, is not deemed filed with
the SEC and is not to be incorporated by reference into any filing of Avigen
under the Securities Act of 1933, as amended, or the Securities Exchange Act of
1934, as amended, whether made before or after the date hereof and irrespective
of any general incorporation language in any such filing.

---

Drug
development is slow, costly and associated with a high failure rate. Therefore,
successful drug development can extend over many years and requires our
executives to employ their judgment in developing long-term operating plans
that:

- identify meaningful treatments for patients,
- effectively demonstrate the safety and efficacy of our products,
  and
- protect our intellectual property and optimize the use of our financial
  resources in order to maximize value retention for our stockholders.

The
Committee believes that in determining compensation, management performance
should be evaluated against specific strategic objectives that create
shareholder value. Complete achievement of these strategic objectives may extend
beyond a given compensation period; therefore, the Committee must use its
discretionary judgment based on the experience and knowledge within the industry
of its members, in assessing the quality of managements performance within an
established framework of general parameters for annual compensation.

Compensation Components

The
Committee draws on a number of reference sources to assist in the evaluation of
the various components of executive compensation. One source is industry data
compiled in the Radford Biotechnology Survey which represents a nationally-based
assessment of executive compensation widely used within the pharmaceutical and
biotechnology industry sectors. The Committee generally focuses on regional data
from companies in the San Francisco Bay Area and targets compensation levels
that fall within the 50th and 70th percentiles reported for
comparable positions based on the Committees subjective determination as to the
appropriate range to attract and retain our executives given the size of our
company. In addition, the Committee examines performance compensation packages
of a number of selected companies that develop products for similar neurological
indications or that are at a similar employee size and development stage. In
2007, this group consisted of Acorda Therapeutics, Inc., XenoPort, Inc.,
Renovis, Inc., Pain Therapeutics, and Palatin Technologies, Inc., however, in
2008, given the companys immediate efforts to preserve cash in response to the
termination of the AV650 program, the Committee, with the support of management,
determined not to take any immediate actions on compensation for fiscal 2008,
and so the Committee did not conduct a competitive analysis of compensation
packages from other companies.

To establish
the relationship between executive compensation and the creation of stockholder
value, the Committee subjectively evaluates the success of the management team
as a whole and each individual executives performance in contributing to
achieving the companys strategic objectives. The Committee applies its
assessment within the framework of our compensation program which defines a
discretionary range in which to determine individual compensation adjustments
for each executive officer. Our compensation program consists of three principal
components: salary, short-term incentive compensation consisting of incentive
bonus payments, and long-term incentive compensation consisting of equity
grants. Each year, the Committee reviews executive officer compensation using
summary tally sheets that show for each of the executive officers the
following: (a) summary of total compensation; (b) each element of current
compensation; and (c) cumulative amount of all previously issued equity awards.

Base
Salary.The Committee reviews each executives base salary annually. Among the
factors taken into consideration are (1) individual performance, (2) corporate
performance measured against strategic objectives, (3) levels of responsibility,
(4) prior experience, (5) breadth of knowledge of the industry, and (6)
competitive pay practices examined from industry source material discussed
above. The Committee does not assign any specific weighting to these various
factors when determining base salary.

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Incentive
Bonus.The Committee sets target incentive
levels annually for each executive officer in consultation and discussion with
our chief executive officer, other than for his own target incentive level.
Ordinarily, the Committee considers industry data compiled by Radford and
determines the appropriate level of target incentive bonus award for our chief
executive officer and for our other executive officers as a percentage of their
respective base salaries based on the Committees subjective determination as to
the appropriate range to attract and retain our executive officers given the
size of the company, assigning the actual percentage within this range based
upon the level of each executive officers responsibility and experience. The
Committee determines actual bonus payments based on subjective assessments of
the performance of management and individual officers in achieving the companys
strategic objectives, applied to these target incentive levels. As a function of
this process, the Committee met several times throughout the year with Dr.
Chahine to review the status of the management teams individual contributions.
The 2008 strategic objectives against which corporate performance was intended
to be measured are discussed below under 2008 Performance.

The
Committee establishes the companys strategic objectives in discussions with our
chief executive officer at the beginning of the compensation period to ensure
that its performance evaluations at the end of the compensation period reflect
the strategic priorities of the company to create value for our stockholders.
Ordinarily, our chief executive officer reviews the performance of the company
and of each executive officer, other than his own, with the Committee at the end
of the compensation period and makes recommendations to the Committee for its
review and final determination.

Equity
Incentives.The Committee is responsible for
making stock option grants under Avigens 2006 Equity Incentive Plan (the
2006 Plan), and believes that long-term stockholder value is best achieved
through an ownership culture among all our employees, particularly our
executives, through grants of stock-based awards.

The
Committee grants stock-based awards under the 2006 Plan with multi-year vesting
periods designed as incentives to retain key employees to continue in the employ
of Avigen. Through option grants, executives receive significant equity
incentives to build long-term stockholder value. The exercise price of options
granted under the 2006 Plan is 100% of fair market value of the underlying stock
on the date of grant. Employees receive value from these grants only if Avigens
common stock appreciates over the long-term. The size of option grants is
determined based primarily on Avigens philosophy of significantly linking
executive compensation with stockholder interests, the individual criteria set
forth below, and the Committees use of industry sources in order to be
knowledgeable of compensation practices for companies of a similar size and
development stage in the biotechnology and pharmaceutical industries.
Historically, the Committee does not target any specific level as compared to
industry average in determining stock option grants.

Change in
Control Arrangements.The Board of Directors,
upon the recommendation of the Committee, established a Management Transition
Plan (Transition Plan) in 1998, which was amended in March 2005 and again in
October 2008. The Transition Plan is intended to retain key employees and enable
executive officers to represent stockholder interests during periods involving a
possible change in control of Avigen, and to provide severance benefits in the
event of termination of employment without cause. The Transition Plan is
designed to protect the earned benefits of key employees, including executive
officers, against adverse changes that may result from a change in control of
Avigen or termination without cause. The level of payments provided under the
agreement for executives reflects the Committees subjective view, based upon
its experience, of comparable benefits offered to executives under change of
control arrangements at other companies within the industry in a similar
development stage. Each of our named executive officers are participants in the
plan and will receive the following benefits if their employment is
involuntarily terminated, or they resign as a result of a constructive
termination, as defined under the Plan:

- 15 months base salary (21 months in the case of Dr. Chahine);
- extended option exercisability of two years;
- full accelerated vesting of outstanding stock options; and
- 15 months (18 months in the case of Dr. Chahine) health benefits payments,
  or until such earlier date as the executive officer secures subsequent
  employment that provides substantially similar health benefits.

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In October
2008, the Board amended the Transition Plan to comply with certain changes in
federal tax regulations that were required to be made before December 31, 2008,
and at the same time, the Committee reviewed benefit levels offered by other
companies within the industry similar to Avigen. Based on this review, theCommittee adjusted the benefits included in the
Transition Plan by adding an additional three months of severance benefits for
each executive officer and extending those benefits to circumstances in which an
executive officer was terminated without cause. The amendments were adopted to
make the Transition Plan comparable to benefits offered by companies similar to
Avigen, as without this security, we were at risk of losing executive talent
necessary to preserve the value of the companys assets.

In March
2009, Avigens Board announced its intention to develop a plan to maximize
Avigens liquidation value. The Board determined that Avigen no longer needed to
retain the services of a majority of its employees, including three executive
officers, Dr. Chahine, Mr. Coffee and Ms. Thomson, and reduced Avigens
headcount accordingly. As a result of these actions, Dr. Chahine, Mr. Coffee and
Ms. Thomson were terminated without cause, triggering their respective benefits
under the Transition Plan.

2008 Performance

At the
beginning of the year, the Committee determined to base its assessment of
Avigens overall performance for the fiscal year ended December 31, 2008 on the
following strategic objectives:

- Quality data from Phase II clinical development progress of
  AV650;
- Responsible management of finances;
- Clinical development progress of AV411;
- Development and progress toward clinical testing of AV513;
- Evaluation, identification and development of new product candidates for
  clinical testing, including proprietary analogs for AV411; and
- Execution of a strategic plan that efficiently manages financial and
  staffing resources to support the research and development needs of the
  company, including raising additional capital for clinical testing.

Historically, the Committee applies its
discretion in determining a subjective evaluation of Avigens overall
performance. For fiscal 2008, the Committee took into consideration the
performance of management against all the 2008 strategic objectives, including
the quality execution of the AV650 Phase II clinical trial, responsible
management of finances, development progress of AV411, and the successful sale
of Avigens early-stage AV513 program for $7 million, and authorized the accrual
of $250,000 for bonus payments to executive officers. In April 2009, the
Committee allocated the bonus pool to Avigens current and former executive
officers.

Bonus
payments for the year ended December 31, 2008 were determined for each
individual executive officer based on target bonus payments that represented a
percent of base salary between 35% and 45%. Target bonus payments were
subsequently weighted so that the bonus payments received were based on the
assessments of the achievement of corporate performance objectives as well as
the subjective determination by the Committee of the executive officers
achievement of individual performance objectives.

2009 Compensation

The
Committee, with the support of management, has determined (given the current
business environment) not to adjust base salaries for 2009, other than in
connection with the promotion of Ms. Thomson to Vice President, General Counsel.
Effective January 1, 2009. Ms. Thomsons base salary was increased to $267,931.
The Committee has not yet finalized or determined the relative weighting of
strategic objectives to be used as the basis for its evaluation of managements
performance for fiscal 2009.

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SUMMARYCOMPENSATIONTABLE

The
following table shows for the fiscal years ended December 31, 2008, 2007 and
2006, compensation awarded to or paid to, or earned by, Avigens Chief Executive
Officer, Chief Financial Officer and its three other most highly compensated
executive officers at December 31, 2008 (the Named Executive Officers).

Summary Compensation
Table

|                                   |  |      |  |        |         |       |  | Option  |         | All Other    |  |           |        
|---------------------------------- |  | ---- |  | ------ | ------- | ----- |  | ------- | ------- | ------------ |  | --------- | -------
|                                   |  |      |  | Salary |         | Bonus |  | Awards  |         | Compensation |  |          
|Name and Principal
      Position  |  | Year |  | ($)    |         | ($)   |  | ($) (2) |         | ($) (3)      |  | Total ($)
|Kenneth G. Chahine, President      |  | 2008 |  | $      | 443,251 |       |  | $       | 80,982  | (1)          |  | $         | 341,318
|and Chief Executive Officer (4)    |  | 2007 |  |        | 426,613 |       |  |         | 158,380 |              |  |           | 333,763
|                                   |  | 2006 |  |        | 407,239 |       |  |         | 95,000  |              |  |           | 271,027
|                                   |  |      |  |        |         |       |  |         |         |              |  |           |        
|Andrew A.
      Sauter, Chief      |  | 2008 |  |        | 267,931 |       |  |         | 42,725  | (1)          |  |           | 208,961
|Financial
      Officer (5)        |  | 2007 |  |        | 238,625 |       |  |         | 68,903  |              |  |           | 166,461
|                                   |  | 2006 |  |        | 229,017 |       |  |         | 28,000  |              |  |           | 98,733 
|                                   |  |      |  |        |         |       |  |         |         |              |  |           |        
|Michael D. Coffee, Chief           |  | 2008 |  |        | 313,903 |       |  |         | 50,978  | (1)          |  |           | 281,150
|Business Officer (4)               |  | 2007 |  |        | 302,120 |       |  |         | 90,636  |              |  |           | 237,876
|                                   |  | 2006 |  |        | 288,400 |       |  |         | 69,000  |              |  |           | 152,547
|                                   |  |      |  |        |         |       |  |         |         |              |  |           |        
|Kirk W. Johnson,
      Ph.D., Vice |  | 2008 |  |        | 278,528 |       |  |         | 39,579  | (1)          |  |           | 249,062
|President
      Research and       |  | 2007 |  |        | 248,824 |       |  |         | 74,025  |              |  |           | 282,000
|Development
      (6)              |  | 2006 |  |        | 237,524 |       |  |         | 46,000  |              |  |           | 192,092
|                                   |  |      |  |        |         |       |  |         |         |              |  |           |        
|M. Christina Thompson, J.D.,       |  | 2008 |  |        | 221,524 |       |  |         | 35,736  | (1)          |  |           | 242,283
|Vice President, General            |  | 2007 |  |        | 239,861 |       |  |         | 65,062  |              |  |           | 234,067
|Counsel and Secretary (4)          |  | 2006 |  |        | 239,444 |       |  |         | 46,000  |              |  |           | 162,436

(1)In 2008, the Compensation Committee
authorized the accrual of $250,000 for bonus payouts to executive officers for
2008. In April 2009, the Compensation Committee authorized bonus payments from
that pool for the year ended December 31, 2008.

(2) The amounts shown in this column
represent the dollar amounts recognized for financial statement reporting
purposes for each fiscal year ended December 31, in accordance with FAS 123(R),
excluding an estimate of forfeitures related to service-based vesting
conditions, and thus include amounts from awards granted in and prior to 2008.
Assumptions used in the calculation of these amounts are described in the notes
to Avigens audited financial statements for the fiscal year ended December 31,
2008, which will be included in Avigens Annual Report on Form 10-K expected to
be filed with the SEC on March 16, 2009. All grants were made subject to
individual award agreements, the form of which was previously filed with the
SEC.

(3) Except as otherwise indicated,
represents insurance premiums paid by Avigen with respect to supplemental
long-term care insurance for the benefit of the Named Executive Officer and up
to $2,500 of matching contributions to Avigens 401(k) savings plan.

(4) Avigen terminated the employment of
each of Dr. Chahine, Mr. Coffee and Ms. Thomson on March 26, 2009 without cause.

(5) On March 26, 2009, Avigen appointed
Mr. Sauter as President and Chief Executive Officer, in addition to his
remaining Chief Financial Officer.

(6) On March 26, 2009, Avigen appointed
Dr. Johnson to be Secretary, in addition to his other functions.

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Item 12.Security Ownership of Certain Beneficial Owners and Management
and Related Stockholder Matters

The
information required by this Item with respect to security ownership of certain
beneficial owners and management is set forth in the Proxy Statement under the
caption, Security Ownership of Certain Beneficial Owners and Management. Such
information is incorporated herein by reference.

In November
2008, Biotechnology Fund, L.P. and certain of its affiliates (collectively,
BVF), purchased approximately 29% of our outstanding shares of common stock.
In January 2009, BVF gave notice to Avigen that it was calling a special meeting
of our stockholders for the purpose of removing our entire Board of Directors,
without cause, and replacing it with four nominees selected by BVF. Also in
January 2009, BVF launched a tender offer to acquire the remaining outstanding
shares of our common stock for $1.00 per share, contingent on BVF being
successful in removing our entire Board of Directors, without cause, and
replacing it with their four nominees, and the redemption of the preferred stock
purchase rights under our shareholder rights agreement. On March 27, 2009, we
held a special meeting of our stockholders where BVF failed to garner enough
votes to remove our entire Board of Directors. As a result, BVFs nominees were
not elected and BVF withdrew its tender offer.

EQUITY COMPENSATION PLAN
INFORMATION

The
following table provides certain information with respect to all of Avigens
equity compensation plans in effect as of December 31, 2008:

|                                             |                                |                         | **Number of securities** 
|-------------------------------------------- | ------------------------------ | ----------------------- | -------------------------
|                                             |                                |                         | **remaining available**  
|                                             | **Number of
      securities** | Weighted-average        | **for future issuance**  
|                                             | **to be issued
      upon**    | exercise price
      of | **under equity**         
|                                             | **exercise
      of**          | outstanding             | **compensation plans**   
|                                             | **outstanding
      options,** | options,                | **(excluding securities**
|                                             | **warrants and
      rights**  | warrants and            | **reflected in column**  
|                                             | **(1)**                        | rights                  | **(a))(2)**              
|Plan Category                                | **(a)**                        | (b)                     | **(c)**                  
|Equity compensation
      plans              |                                |                         |                          
|approved by
      security holders           | 3,165,283                      | $                       | 5.80                     
|Equity compensation plans not
      approved |                                |                         |                          
|by security
      holders                    | 977,041                        | $                       | 8.68                     
|Total                                        | 4,142,324                      | $                       | 6.48                     

(1) Our 2000 Equity Incentive Plan (the
2000 Plan) was adopted in 2000 without stockholder approval. The 2000 Plan was
amended and restated as our 2006 Equity Incentive Plan (the 2006 Plan), which
amendment and restatement was approved by our stockholders on May 31, 2006. The
number of shares subject to options outstanding under plans not approved by our
stockholders reflects options granted pursuant to the 2000 Plan prior to May 31,
2006, which number of shares is not reflected as outstanding under compensation
plans approved by our stockholders.

(2) Reflects shares available for grant
under our 2006 Plan.

***2000 Equity Incentive
Plan***

Prior to the
amendment and restatement of Avigens 2000 Equity Incentive Plan (the
2000 Plan) as the 2006 Equity Incentive Plan, the 2000 Plan provided for the
grant of nonqualified stock options, stock bonuses and restricted stock purchase
awards (collectively, stock awards). An aggregate of 5,000,000 shares of
common stock had been reserved for issuance under the 2000 Plan. Stock awards
could be granted under the 2000 Plan to employees (including officers),
directors and consultants of Avigen and its affiliates; provided, however, that
the aggregate number of shares issued pursuant to stock awards granted to
officers and directors under the 2000 Plan could not exceed 40% of the number of
shares reserved for issuance under the 2000 Plan, except that stock awards
granted to officers prior to their employment by Avigen as an inducement to
entering into employment contracts with Avigen were not included in the 40%
limitation. The exercise price of options and restricted stock purchase awards
could not be less than 85% of the fair market value of the stock on the date of
grant. Stock bonuses could be awarded in consideration for past services
actually rendered to Avigen or its affiliates.

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Vesting.Stock awards granted under
the 2000 Plan may become exercisable (in the case of options) or released from a
repurchase option in favor of Avigen (in the case of stock bonuses and
restricted stock purchase awards) in cumulative increments (vest) as
determined by the Board. The Board has the power to accelerate the time during
which stock awards may vest or be exercised. In addition, options granted under
the 2000 Plan may permit exercise prior to vesting, but in such event the
participant may be required to enter into an early exercise stock purchase
agreement that allows Avigen to repurchase unvested shares, generally at their
exercise price, should the participants service terminate before
vesting.

Term. The term of options granted
under the 2000 Plan was determined by the Board in its discretion. Options under
the 2000 Plan generally terminate three months after termination of the
participants service, subject to extension in certain circumstances.

Effect of
Certain Corporate Events.The 2000 Plan
provides that, in the event of a dissolution, liquidation or sale of
substantially all of the assets of Avigen, specified type of merger, or other
corporate reorganization (a change in control), any surviving corporation must
either assume any stock awards outstanding under the 2000 Plan or substitute
similar stock awards for those outstanding under the 2000 Plan, or else the
outstanding stock awards will continue in full force and effect. In the event
that any surviving corporation declines to assume or continue the stock awards
outstanding under the 2000 Plan, or to substitute similar stock awards, then,
with respect to stock awards held by persons then performing services as
employees, directors, or consultants of Avigen, the vesting and the time during
which these stock awards may be exercised will be accelerated in
full.

Item 13.Certain Relationships and Related Transactions, and Director
Independence

The
information required by this Item is set forth in the Proxy Statement under the
headings Information Regarding the Board of Directors and Corporate Governance
 Independence of the Board of Directors and Related Person Transactions
Policy and Procedures. Such information is incorporated herein by reference.

Item 14.Principal Accounting Fees and Services

The
following table is a summary of the fees billed to Avigen by Odenberg, Ullakko,
Muranishi & Co. LLP (OUM) for the fiscal years ended December 31, 2008 and
2007 for professional services rendered as Avigens registered public
accountant.

|                         |  | Fiscal Year Ended
|------------------------ |  | -----------------
|                         |  | December 31,     
|                         |  | 2008             
|Audit Fees               |  | $                
|Audit-Related
      Fees |  |                  
|Tax Fees                 |  |                  
|All Other
      Fees     |  |                  
|Total Fees               |  | $                

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Audit
Fees.Consists of fees for professional
services rendered for the audit of Avigens annual financial statements and
services that are normally provided by OUM in connection with regulatory filings
or engagements.

Audit-Related Fees.During the fiscal
years ended December 31, 2008 and 2007, no audit-related services were performed
by OUM.

Tax Fees.Consists of fees for professional services
for tax compliance, tax advice and tax planning by OUM for the tax years ended
December 31, 2008 and 2007.

All Other
Fees.During the fiscal years ended December
31, 2008 and 2007, there were no other fees for services rendered by
OUM.

All fees described above were
approved by the Audit Committee.

Pre-Approval Policies and Procedures

Avigens
Audit Committee pre-approves all audit and permissible non-audit services
provided by Avigens independent registered public accounting firm. These
services may include audit services, audit-related services, tax services and
other services. Prior to engaging Avigens independent registered public
accounting firm to render an audit or permissible non-audit service, the Audit
Committee specifically approves the engagement of Avigens independent
registered public accounting firm to render that service. Accordingly, Avigen
does not engage its independent registered public accounting firm to render
audit or permissible non-audit services pursuant to pre-approval policies or
procedures or otherwise, unless the engagement to provide such services has been
approved by the Audit Committee in advance. As such, 100% of the services
described in the categories above for which OUM was engaged were approved by the
Audit Committee in advance of the rendering of those services. The Audit
Committee has determined that the rendering of the services other than audit
services by OUM is compatible with maintaining the registered public accounting
firms independence, respectively.

Consistent
with Section 10A(i)(2) of the Securities Exchange Act of 1934, as added by
Section 202 of the Sarbanes-Oxley Act of 2002, we are responsible for listing
the non-audit services approved by our Audit Committee to be performed by OUM,
our external auditor. Non-audit services are defined as services other than
those provided in connection with an audit or a review of our financial
statements. Our Audit Committee has approved our recurring engagements of
non-audit services of OUM for the preparation of tax returns and tax advice in
preparing for and in connection with such filings.

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SIGNATURES

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

| | AVIGEN, INC.
| | ------------
| |             
| |             
| | By:         
| |             
| |             
| |             

Dated: April 29, 2009

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Exhibit Index

To Amendment No. 1 to Annual Report
on Form 10-K/A

|Exhibit |  | Description of document                                                                                 
|------- |  | --------------------------------------------------------------------------------------------------------
|31.1    |  | Certification by Chief Executive Officer Pursuant to
      Section 302 of the Sarbanes-Oxley Act of 2002
|31.2    |  | Certification by Chief Financial Officer Pursuant to Section 302 of
      the Sarbanes-Oxley Act of 2002

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