<PAGE>   1
                                                                   EXHIBIT 10.47


                       SECOND AMENDMENT TO LEASE AGREEMENT

This Second Amendment to Lease Agreement (the "Amendment") is made and entered
into as of February 12, 2001, by and between LINCOLN-RECP EMPIRE OPCO, LLC, a
California limited liability company ("Landlord") and AVIGEN, INC., a Delaware
corporation ("Tenant"), with reference to the following facts.

                                    RECITALS

A.      Landlord and Tenant have entered into that certain Lease Agreement dated
        as of November 2, 2000, as amended by that certain First Amendment to
        Lease Agreement dated as of December 1, 2000 (collectively, the "Lease")
        for the leasing of certain premises consisting of approximately 67,482
        rentable square feet located at 1301 Harbor Bay Parkway, Alameda,
        California (the "Premises") as such Premises are more fully described in
        the Lease, for a term commencing on December 1, 2000, and expiring on
        November 30, 2010.

B.      The terms of the Lease were for a "full-service" lease; Tenant wishes to
        amend the Lease to be a "triple net" Lease at a lower rental rate, and
        Landlord is agreeable to the same.

C.      Landlord and Tenant now wish to amend the Lease upon and subject to each
        of the terms, conditions and provisions set forth herein.

NOW, THEREFORE, in consideration of the foregoing and for other good and
valuable consideration, the receipt and adequacy of which are hereby
acknowledged, Landlord and Tenant agree as follows:

        1. RECITALS: Landlord and Tenant agree that the above recitals are true
and correct and are hereby incorporated herein as though set forth in full.

        2. MODIFICATIONS TO LEASE: Effective as of December 1, 2000 (the
"Effective Date"), the Lease is hereby modified as follows:

                2.1 BASE RENT.

                ARTICLE 3 - BASE RENT of the Lease is hereby amended as follows:

                                The first table set forth in Section 8. Base
Rent (Article 3) of the Summary of Basic Lease Information in the Lease is
hereby revised in accordance with the following schedule:

<TABLE>
<CAPTION>
              ----------------------- ----------- ----------------------- ----------------------
                       TERM           SQUARE        ANNUAL RENTAL RATE     MONTHLY INSTALLMENT
                                         FEET      PER RENTABLE SQUARE        OF BASE RENT
                                                           FOOT
              ----------------------- ----------- ----------------------- ----------------------
              <S>                     <C>         <C>                     <C>
                12/1/00 -- 11/30/01     34,537            $17.62               $ 50,711.83
              ----------------------- ----------- ----------------------- ----------------------
                12/1/01 -- 11/30/02     34,537            $18.34               $ 52,784.05
              ----------------------- ----------- ----------------------- ----------------------
                12/1/02 -- 12/31/02     34,537            $19.06               $ 54,856.27
              ----------------------- ----------- ----------------------- ----------------------
                 1/1/03 -- 11/30/03     67,482            $19.06               $107,183.91
              ----------------------- ----------- ----------------------- ----------------------
                12/1/03 -- 11/30/04     67,482            $19.90               $111,907.65
              ----------------------- ----------- ----------------------- ----------------------
                12/1/04 -- 11/30/05     67,482            $20.62               $115,956.57
              ----------------------- ----------- ----------------------- ----------------------
                12/1/05 -- 11/30/06     67,482            $21.46               $120,680.31
              ----------------------- ----------- ----------------------- ----------------------
                12/1/06 -- 11/30/07     67,482            $22.30               $125,404.05
              ----------------------- ----------- ----------------------- ----------------------
                12/1/07 -- 11/30/08     67,482            $23.14               $130,127.79
              ----------------------- ----------- ----------------------- ----------------------
                12/1/08 -- 11/30/09     67,482            $23.98               $134,851.53
              ----------------------- ----------- ----------------------- ----------------------
                12/1/09 -- 11/30/10     67,482            $24.94               $140,250.09
              ----------------------- ----------- ----------------------- ----------------------
</TABLE>

                      Base Rent for the A Remaining Premises is waived by the
               Landlord for the period from the RPA Commencement Date through
               the RPB Commencement Date. From and after the RPB Commencement
               Date, Tenant shall pay to Landlord Base Rent for both the RPA
               Remaining Premises and the RPB Remaining Premises at the monthly
               rate of $0.99 per rentable square foot, or Thirty-two Thousand
               Five Hundred Sixty Dollars and Sixty-four Cents ($32,560.64),
               through May 31, 2002; and thereafter Tenant shall pay to Landlord
               Base Rent for both the RPA Remaining Premises and the RPB
               Remaining Premises at the monthly rate of $1.06 per rentable
               square foot, or Thirty-four Thousand Eight Hundred Sixty-six
               Dollars and Seventy-nine Cents ($34,866.79).

                      The second table set forth in Section 8. Base Rent
               (Article 3) of the Summary of Basic Lease Information in the
               Lease (for Base Rent for the "Remaining Premises" from the "RP
               Commencement Date" through December 31, 2002), is hereby revised
               in accordance with the following schedule:

<TABLE>
<CAPTION>
              ----------------------- ---------------- ------------------------- --------------
                       TERM              REMAINING       REMAINING PREMISES -       MONTHLY
                                         PREMISES       ANNUAL RENTAL RATE PER    INSTALLMENT
                                        SQUARE FEET      RENTABLE SQUARE FOOT    OF BASE RENT
              ----------------------- ---------------- ------------------------- --------------
              <S>                     <C>              <C>                       <C>
                 3/1/01 - 5/31/02         32,945                $11.86            $32,560.64
              ----------------------- ---------------- ------------------------- --------------
                6/1/02 - 12/31/02         32,945                $12.70            $34,866.79
              ----------------------- ---------------- ------------------------- --------------
</TABLE>

<PAGE>   2

                      Advance Rent (Section 3.1) shall be Fifty Thousand Seven
               Hundred Eleven Dollars and Eighty-three Cents ($50,711.83).

               2.2 DELETION OF BASE YEAR. Section 9.1 -- Base Year for Tenant's
        Share of Direct Expenses -- of the Summary of Basic Lease Information in
        the Lease, and Section 4.3.1 of the Lease are hereby deleted in their
        entirety, it being the intention of the parties that there shall be no
        "Base Year" in the Lease, and that Tenant shall pay Direct Expenses
        without any deduction for Base Year expenses.

                2.3 ADDITIONAL RENT. Section 4.1 of the Lease is hereby deleted
        in its entirety and replaced by the following:

                      4.1 ADDITIONAL RENT. Commencing on the Lease Commencement
               Date and continuing throughout the balance of the Lease Term,
               Tenant shall pay as additional rent the "Tenant's Share", as
               defined in Section 4.3.8, of Direct Expenses. Such additional
               rent, together with any and all other amounts payable by Tenant
               to Landlord pursuant to the terms of this Lease (including,
               without limitation, pursuant to Article 6), shall be hereinafter
               collectively referred to as the "Additional Rent." The Base Rent
               and Additional Rent are herein collectively referred to as the
               "Rent." All amounts due under this Article 4 as Additional Rent
               shall be payable for the same periods and in the same manner,
               time and place as the Base Rent. Without limitation on other
               obligations of Tenant which shall survive the expiration of the
               Lease Term, the obligations of Tenant to pay the Additional Rent
               provided for in this Article 4 which is properly attributable to
               the Lease Term shall survive the expiration or earlier
               termination of the Lease Term.

               2.4 OPERATING EXPENSES. The first paragraph of Section 4.3.5 of
        the Lease is hereby deleted in its entirety and replaced by the
        following:

                      4.3.5 "Operating Expenses" shall mean all expenses, costs
               and amounts of every kind and nature which Landlord shall pay
               during any Expense Year because of or in connection with the
               ownership, management, maintenance, repair, replacement,
               restoration or operation of the Building, Complex and Real
               Property, including, without limitation, any amounts paid for:
               (i) the cost of licenses, certificates, permits and inspections,
               and the cost of contesting the validity or applicability of any
               governmental enactments which may affect Operating Expenses, and
               the costs incurred in connection with implementation and
               operation of any transportation system management program or
               similar program required by any governmental authority; (ii) the
               cost of insurance carried by Landlord, in such amounts as
               Landlord may reasonably determine or as may be required by any
               mortgagees or the lessor of any underlying or ground lease
               affecting the Real Property, the Complex and/or the Building,
               including any commercially reasonable deductibles; (iii) the cost
               of exterior landscaping, exterior relamping, supplies, tools,
               equipment and materials, and all fees, charges and other costs
               (including consulting fees, legal fees and accounting fees)
               incurred by Landlord in connection with the management,
               operation, repair and maintenance of the Building, the Complex
               and Real Property; (iv) the cost of parking area repair,
               restoration, and maintenance; (v) any equipment rental agreements
               or management agreements (including the cost of any management
               fee and the fair rental value of any office space provided
               thereunder); (vi) wages, salaries and other compensation and
               benefits of all persons directly engaged (whether or not 100% of
               such person's efforts are devoted to this Building, Complex and
               Real Property, provided that only the portion attributable to
               this Building, Complex and Real Property shall be included in
               Operating Expenses) in the operation, management, maintenance or
               security of the Building, the Complex and the Real Property, and
               employer's Social Security taxes, unemployment taxes or
               insurance, and any other taxes which may be levied on such wages,
               salaries, compensation and benefits; (vii) payments under any
               easement, license, operating agreement, declaration, restrictive
               covenant, underlying or ground lease (excluding rent), or
               instrument pertaining to the sharing of costs by the Building,
               Complex or Real Property; (viii) the cost of alarm and security
               service (if any security service is provided by Landlord), fire
               protection and life/safety systems and services, exterior window
               cleaning, trash removal, maintenance and replacement of curbs and
               walkways, repair to roofs and re-roofing; (ix) any and all
               levies, charges, fees and/or assessments payable to any
               applicable owner's association and/or condominium association
               with respect to the Complex; (x) amortization (including interest
               on the unamortized cost) of the cost of acquiring or the rental
               expense of personal property used by Landlord in the maintenance,
               operation and repair of the Building, Complex and Real Property;
               and (xi) the cost of any capital improvements or other costs (I)
               which are intended as a labor-saving device or to effect other
               economies in the operation or maintenance of the Building,
               Complex and Real Property, to the extent that the same result in
               savings, and (II) made to the Building, Complex or Real Property
               after the Lease Commencement Date that are required under any
               governmental law or regulation adopted subsequent to the
               Commencement Date, or (III) which are reasonably determined by
               Landlord to be in the best interests of the Building, the Complex
               and/or the Real Property; provided, however, that if any such
               cost described in (I), (II) or (III) above, is a capital
               expenditure, such cost shall be amortized (including interest on
               the unamortized cost) over its estimated useful life as Landlord
               shall reasonably determine, which estimated useful life shall be
               comparable to that used by landlords of comparable buildings in
               the vicinity of the Complex. If Landlord is not furnishing any
               particular work or service (the cost of which, if performed by
               Landlord, would be included in Operating Expenses) to a tenant
               who has undertaken to perform such work or service in lieu of the
               performance thereof by Landlord, Operating Expenses shall be
               deemed to be increased by an amount equal to the additional
               Operating Expenses which would reasonably have been incurred
               during such period by Landlord if it had at its own expense
               furnished such work or service to such tenant. If the Building or
               the Complex is not fully occupied during all or a portion of any
               Expense Year, Landlord shall make an appropriate adjustment to
               the variable components of Operating Expenses for such year or
               applicable portion thereof, employing sound accounting and
               management principles, to


                                       2
<PAGE>   3

               determine the amount of Operating Expenses that would have been
               paid had the Building and/or the Complex been fully occupied; and
               the amount so determined shall be deemed to have been the amount
               of Operating Expenses for such year, or applicable portion
               thereof. Landlord shall have the right, from time to time, to
               equitably allocate some or all of the Operating Expenses among
               different tenants of the Building and/or the Complex (the "Cost
               Pools"). Such Cost Pools may include, without limitation, the
               office space tenants and retail space tenants of the Building
               and/or the Complex.

               In addition, the last sentence of the second paragraph of Section
        4.3.5 and all of Section 4.3.7.2 are hereby deleted in their entirety.

               2.5 SYSTEMS AND EQUIPMENT. Section 4.3.6 of the Lease is hereby
        deleted in its entirety and replaced by the following:

                      4.3.6 "Systems and Equipment" shall mean any plant,
               machinery, transformers, duct work, cable, wires, and other
               equipment, facilities, and systems designed to supply heat,
               ventilation, air conditioning and humidity or any other services
               or utilities, or comprising or serving as any component or
               portion of the electrical, gas, steam, plumbing, sprinkler,
               communications, alarm, or security systems or equipment, or any
               other mechanical, electrical, electronic, computer or other
               systems or equipment which serve the Premises in whole or in
               part.

               2.6 TENANT'S SHARE OF DIRECT EXPENSES. Section 4.4.1 and Section
        4.4.2.1 of the Lease are hereby deleted in their entirety and replaced
        by the following:

                      4.4.1 TENANT'S SHARE OF DIRECT EXPENSES. For any Expense
               Year ending or commencing within the Lease Term, Tenant shall pay
               to Landlord, in the manner set forth in Section 4.4.2, below, and
               as Additional Rent, Tenant's Share of Direct Expenses for such
               Expense Year.

                      4.4.2  STATEMENT OF ACTUAL DIRECT EXPENSES AND PAYMENT BY
               TENANT.

                             4.4.2.1 Landlord shall endeavor to give to Tenant
               on or before the first day of the sixth month following the end
               of each Calendar Year, a statement (the "Statement") which shall
               state the Direct Expenses incurred or accrued for such preceding
               Expense Year. Upon receipt of the Statement for each Expense Year
               ending during the Lease Term, Tenant shall pay, with its next
               installment of Base Rent due, the full amount of the Direct
               Expenses for such Expense Year, less the amounts, if any, paid
               during such Expense Year as the "Estimate," as that term is
               defined in Section 4.4.3 of this Lease. In the event that the
               amount paid by Tenant during such Expense Year as an Estimate
               exceeds the actual Direct Expenses, Landlord shall remit such
               difference to Tenant within thirty (30) days. The failure of
               Landlord to timely furnish the Statement for any Expense Year
               shall not prejudice or prevent Landlord from enforcing its rights
               under this Article 4. Even though the Lease Term has expired and
               Tenant has vacated the Premises, when the final determination is
               made of Tenant's Share of the Direct Expenses for the Expense
               Year in which this Lease terminates, Tenant shall immediately pay
               to Landlord the full amount of the Direct Expenses for such
               Expense Year, less the amounts, if any, paid during such Expense
               Year as the Estimate, and any overpayment by Tenant shall be
               returned to Tenant within thirty (30) days.

               2.7 STATEMENT OF ESTIMATED DIRECT EXPENSES. Section 4.4.3 of the
        Lease is hereby deleted in its entirety and replaced by the following:

                      4.4.3 STATEMENT OF ESTIMATED DIRECT EXPENSES. In addition,
               Landlord shall endeavor to give Tenant a yearly expense estimate
               statement (the "Estimate Statement") which shall set forth
               Landlord's reasonable estimate (the "Estimate") of what the total
               amount of Direct Expenses for the then-current Expense Year. The
               failure of Landlord to timely furnish the Estimate Statement for
               any Expense Year shall not preclude Landlord from enforcing its
               rights to collect any Estimate under this Article 4. Commencing
               on the Commencement Date, Tenant shall pay, with its next
               installment of Base Rent due, a fraction of the Estimate for the
               then-current Expense Year (reduced by any amounts paid pursuant
               to the last sentence of this Section 4.4.3). Such fraction shall
               have as its numerator the number of months which have elapsed in
               such current Expense Year to the month of such payment, both
               months inclusive, and shall have twelve (12) as its denominator.
               Until a new Estimate Statement is furnished, Tenant shall pay
               monthly, with the monthly Base Rent installments, an amount equal
               to one-twelfth (1/12) of the total Estimate set forth in the
               previous Estimate Statement delivered by Landlord to Tenant.

               2.8 SERVICES AND UTILITIES. Article 6 of the Lease is hereby
        deleted in its entirety and replaced by the following:

               ARTICLE 6 - SERVICES AND UTILITIES

                      6.1 STANDARD TENANT SERVICES. Landlord shall provide the
               following services on all days during the Lease Term, unless
               otherwise stated below.

                             6.1.1 Landlord shall provide adequate electrical
               wiring and facilities for normal general office use as reasonably
               determined by Landlord. Tenant shall bear the cost of power,
               replacement of lamps, starters and ballasts for lighting fixtures
               within the Premises.

                             6.1.2 Landlord shall provide exterior window
               washing services in a manner consistent with other comparable
               buildings in the vicinity of the Building.


                                       3

<PAGE>   4

                             Landlord shall have no responsibility for providing
               the following services, and Tenant shall be responsible for the
               same: (i) heating, ventilation or air-conditioning service,
               supplies, maintenance or repairs; (ii) electrical power, service,
               supplies, maintenance or repairs; (iii) water and sewer; (iv)
               janitorial service or supplies; (v) freight and passenger
               elevator service; (vi) interior landscaping; (vii) plumbing
               service, supplies, maintenance or repairs; or (viii) any other
               utilities.

                      6.2 INTERRUPTION OF USE. Tenant agrees that Landlord shall
               not be liable for damages, by abatement of Rent or otherwise, for
               inability of Tenant to obtain or delay in obtaining any service
               (including telephone and telecommunication services), or for any
               diminution in the quality or quantity thereof; and such inability
               or delays or diminution shall never be deemed to constitute an
               eviction or disturbance of Tenant's use and possession of the
               Premises or relieve Tenant from paying Rent or performing any of
               its obligations under this Lease. Furthermore, Landlord shall not
               be liable under any circumstances for a loss of, or injury to,
               property or for injury to, or interference with, Tenant's
               business, including, without limitation, loss of profits, however
               occurring, through or in connection with or incidental to an
               inability to obtain any of the services or utilities as set forth
               in this Article 6. Notwithstanding the foregoing, if an inability
               to obtain utilities results from the gross negligence or willful
               misconduct of Landlord, or its employees, agents and contractors,
               and not due to any fault or breach by Tenant, and the Premises
               are not usable by Tenant for the conduct of Tenant's business as
               a result thereof, Base Rent and applicable Direct Expenses not
               actually incurred up to that point by Tenant shall be abated for
               the period which commences five (5) business days after the date
               Tenant gives to Landlord notice of such interruption until such
               utilities are restored.


                      6.3    OFFICE AND COMMUNICATIONS SERVICES.

                             6.3.1 Landlord has advised Tenant that certain
               office and communications services may be offered to tenants of
               the Building by a concessionaire under contract to Landlord
               ("Provider"). Tenant shall be permitted to contract with Provider
               for the provision of any or all of such services on such terms
               and conditions as Tenant and Provider may agree. Tenant shall
               also be permitted to obtain office and communications services
               from any other reputable person or entity in the business of
               providing the same (herein called an "Alternate Provider"),
               provided that Landlord shall not be required thereby to make any
               alterations in or to any part of the Building or the use of any
               facilities or equipment of the Building, and provided further
               that no such services provided by an Alternate Provider, or any
               equipment or facilities used or to be used in connection
               therewith shall be incompatible in any respect with, or shall
               interfere with or otherwise impair or adversely affect, the
               operation, reliability or quality of the Building systems or any
               services, equipment or facilities used or operated by Provider or
               any other tenant in the Building.

                             6.3.2 Tenant acknowledges and agrees that: (i)
               Landlord has made no warranty or representation to Tenant with
               respect to the availability of any such services, whether
               provided by Provider or any Alternate Provider, or the quality,
               reliability or suitability thereof; (ii) neither Provider nor any
               Alternate Provider is acting as the agent or representative of
               Landlord in the provision of such services, and Landlord shall
               have no liability or responsibility for any failure or inadequacy
               of such services or any equipment or facilities used in the
               furnishing thereof, or any act or omission of Provider or any
               Alternate Provider or their agents, employees, representatives,
               officers or contractors; (iii) Landlord shall have no
               responsibility or liability for the installation, alteration,
               repair, maintenance, furnishing, operation adjustment or removal
               of any such services, equipment or facilities; and (iv) any
               contract or other agreement between Tenant and Provider or any
               Alternate Provider shall be independent of this Lease, the
               obligations of Tenant hereunder, and the rights of Landlord
               hereunder. Without limiting the generality of the foregoing, no
               default or failure of Provider or any Alternate Provider with
               respect to any such services, equipment, facilities, or under any
               contract or agreement relating thereto, shall have any effect on
               this Lease or give to Tenant any offset or defense to the full
               and timely performance of its obligations hereunder, or entitle
               Tenant to any abatement of Rent or Additional Rent or any other
               payment required to be made by Tenant hereunder, or constitute
               any actual or constructive eviction of Tenant, or otherwise give
               rise to any other claim of any nature against Landlord.

                      6.4 UTILITIES FOR LABORATORY SPACE. In the event Tenant
               constructs a laboratory within the Premises, Tenant shall cause
               such laboratory to be separately metered and shall pay the
               utility companies directly for the cost of any utilities. In the
               event Tenant pays the utility companies directly for the cost of
               any utilities, costs for such utilities shall not be included in
               Direct Expenses.

               2.9 REPAIRS AND MAINTENANCE. Article 7 - Repairs of the Lease is
        hereby deleted in its entirety and replaced by the following:

                      7.     REPAIRS AND MAINTENANCE

                      7.1 TENANT'S REPAIRS AND MAINTENANCE OBLIGATIONS: Except
               for those portions of the Premises to be maintained by Landlord,
               as provided in Sections 7.2 and 7.3 below, Tenant shall, at its
               sole cost and expense, keep and maintain all parts of the
               Premises in good, clean and safe condition and repair, promptly
               making all necessary repairs and replacements, whether ordinary
               or extraordinary, with materials and workmanship of the same
               character, kind and


                                       4
<PAGE>   5

               quality as the original thereof, all of the foregoing to the
               reasonable satisfaction of Landlord including, but not limited
               to, repairing any damage caused by Tenant or any of Tenant's
               Representatives and replacing any property so damaged by Tenant
               or any of Tenant's Representatives. Without limiting the
               generality of the foregoing, Tenant shall be solely responsible
               for promptly maintaining, repairing and replacing (a) all
               mechanical systems, heating, ventilation and air conditioning
               systems exclusively serving the Premises, unless maintained by
               Landlord, (b) all plumbing work and fixtures exclusively serving
               the Premises (from their point of entry into the Premises), (c)
               electrical wiring systems, fixtures and equipment exclusively
               serving the Premises (from their point of entry into the
               Premises), (d) all interior lighting (including, without
               limitation, light bulbs and/or ballasts), (e) all glass, windows,
               window frames, window casements, skylights, interior and exterior
               doors, door frames and door closers located within the Premises,
               (f) all roll-up doors, ramps and dock equipment located within
               the Premises, (g) all tenant signage, (h) lifts for disabled
               persons exclusively serving the Premises, (i) sprinkler systems,
               security systems exclusively serving the Premises, except to the
               extent maintained by Landlord, and (j) all lighting systems,
               partitions, fixtures, equipment, interior painting, interior
               walls and floors and floor coverings, and ceiling tiles and
               fixtures of the Premises and every part thereof (including,
               without limitation, any demising walls contiguous to any portion
               of the Premises). Additionally, Tenant shall be solely
               responsible for performance of the regular removal of trash and
               debris. Tenant shall have no right of access to or right to
               install any device on the roof of the Premises nor make any
               penetrations of the roof of the Premises without the express
               prior written consent of Landlord. Tenant shall obtain and
               maintain throughout the term of this Lease maintenance and
               service contracts for the elevator and for the heating,
               ventilation and air-conditioning system, including periodic
               maintenance therefor, reasonably satisfactory to Landlord, and
               shall provide Landlord with copies thereof and such reasonable
               assurances that such contracts are in full force and effect as
               Landlord may reasonably require.

                      7.2 MAINTENANCE BY LANDLORD: Subject to the provisions of
               Section 7.1 above, and further subject to Tenant's obligation
               under Article 4 to reimburse Landlord, in the form of Additional
               Rent, for the cost and expense of the following described items,
               Landlord agrees to repair and maintain the following items: fire
               protection and life/safety systems and services; the roof and
               roof coverings (provided that Tenant installs no additional air
               conditioning or other equipment on the roof that damages the roof
               coverings, in which event Tenant shall pay all costs relating to
               the presence of such additional equipment); exterior painting of
               the Premises; exterior window cleaning; exterior lighting
               adjacent to the Premises; and the parking areas, pavement,
               landscaping, sprinkler systems, sidewalks, driveways and curbs.
               Notwithstanding anything in this Article 7 to the contrary,
               Landlord shall have the right to either repair or to require
               Tenant to repair any damage to any portion of the Premises caused
               by or created due to any act, omission, negligence or willful
               misconduct of Tenant or any of Tenant Representatives and to
               restore the Premises to the condition existing prior to the
               occurrence of such damage. If Landlord elects to perform such
               repair and restoration work, Tenant shall reimburse Landlord upon
               demand for all costs and expenses incurred by Landlord in
               connection therewith. Tenant shall promptly report, in writing,
               to Landlord any defective condition known to it which Landlord is
               required to repair, and failure to so report any such defect
               shall make Tenant responsible to Landlord for any liability
               incurred by Landlord by reason of such condition, to the extent
               such liability is due to Tenant's failure to so report such
               defect.

                      7.3 LANDLORD'S REPAIRS AND MAINTENANCE OBLIGATIONS:
               Subject to the provisions of Section 7.1 and Articles 25 and 26,
               and except for repairs rendered necessary by the intentional or
               negligent acts or omissions of Tenant or any of Tenant's
               Representatives, Landlord agrees, at Landlord's sole cost and
               expense, to (a) keep in good repair the structural portions of
               the floors, foundations and exterior perimeter and interior load
               bearing walls of the Premises (exclusive of glass and exterior
               doors), and (b) replace the structural portions of the roof of
               the Premises (excluding the roof membrane).

                      7.4 TENANT'S FAILURE TO PERFORM REPAIRS AND MAINTENANCE
               OBLIGATIONS: If Tenant refuses or neglects to repair and maintain
               the Premises and the other areas properly as required herein and
               to the reasonable satisfaction of Landlord, Landlord may, but
               without obligation to do so, at any time make such repairs or
               maintenance without Landlord having any liability to Tenant for
               any loss or damage that may accrue to Tenant's Property or to
               Tenant's business by reason thereof, except to the extent any
               damage is caused by the willful misconduct or gross negligence of
               Landlord or its authorized agents and representatives. If
               Landlord makes such repairs or maintenance, upon completion
               thereof Tenant shall pay to Landlord, as Additional Rent,
               Landlord's costs and expenses incurred therefor. The obligations
               of Tenant hereunder shall survive the expiration of the Term of
               this Lease or the earlier termination thereof. Tenant hereby
               waives any right to repair at the expense of Landlord under any
               applicable Laws now or hereafter in effect with respect to the
               Premises.

        3. EFFECT OF AMENDMENT: Except as modified herein, the terms and
conditions of the Lease shall remain unmodified and continue in full force and
effect. In the event of any conflict between the terms and conditions of the
Lease and this Amendment, the terms and conditions of this Amendment shall
prevail. Tenant hereby renews its obligations to Landlord for the full, prompt
and timely payment of all rents and other sums required to be paid by Tenant
during the term of the Lease as herein modified, and for the full, prompt and
timely performance of, compliance with and observation of all the terms
contained in the Lease as herein modified.

        4. DEFINITIONS: Unless otherwise defined in this Amendment, all terms
not defined in this Amendment shall have the meaning set forth in the Lease.

        5. NO BROKER: Each party warrants and represents to the other that no
real estate broker, sales person, finder or other person has the right to
payment of a commission or fee in connection with this


                                       5
<PAGE>   6

Amendment as a consequence of contacts with such party. Each party shall
indemnify, protect, defend and hold the other harmless from any and all loss,
cost, damage or expense (including attorneys' fees and costs, including fees and
costs on appeal, if any) arising out of or related to claims for a real estate
brokerage commission, finder's fee or similar compensation, based upon
allegations by the claimant that it is entitled to a commission, fee or other
compensation from the indemnified party as a consequence of contacts with the
indemnifying party.

        6. ENTIRE AGREEMENT: The Lease and this Amendment constitute the entire
understanding between the parties with respect to the Premises. No subsequent
amendment will be effective unless it is in writing and executed by the parties.

        7. COUNTERPARTS: This Amendment may be executed in counterparts, each of
which when executed and delivered shall be an original.

        8. AUTHORITY: Subject to the provisions of the Lease, this Amendment
shall be binding upon and inure to the benefit of the parties hereto, their
respective heirs, legal representatives, successors and assigns. Each party
hereto and the persons signing below warrant that the person signing below on
such party's behalf is authorized to do so and to bind such party to the terms
of this Amendment.


IN WITNESS WHEREOF, the parties have executed this Amendment as of the date and
year first above written.

                                           TENANT:

                                           AVIGEN, INC.,
                                           a Delaware corporation



Date:   2/13/01                            By: /s/ JOHN MONAHAN
      -----------------------                 ----------------------------------
                                           Name:   John Monahan
                                                --------------------------------
                                           Title:  CEO
                                                 -------------------------------

Date:   2/13/01                            By: /s/ THOMAS J. PAULSON
     -----------------------                  ----------------------------------
                                           Name:   Thomas J. Paulson
                                                --------------------------------
                                           Title:  VP-Finance, CFO
                                                 -------------------------------




                                           LANDLORD:

                                           LINCOLN-RECP EMPIRE OPCO, LLC,
                                           a California limited liability
                                           company

                                           By: Legacy Partners Commercial, Inc.,
                                           as agent for LINCOLN-RECP EMPIRE
                                           OPCO, LLC,



Date:                                      By: /s/ DEBRA SMITH
     -----------------------                  ----------------------------------
                                           Name:   Debra Smith
                                                --------------------------------
                                           Title:  Senior Vice President
                                                 -------------------------------


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