<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-12-18</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0000932903</issuerCik>
        <issuerName>AVIGEN INC \DE</issuerName>
        <issuerTradingSymbol>AVGN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001361978</rptOwnerCik>
            <rptOwnerName>Southpaw Asset Management LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>FOUR GREENWICH OFFICE PARK</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GREENWICH</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06831</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001385743</rptOwnerCik>
            <rptOwnerName>Southpaw Credit Opportunity Master Fund, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>FOUR GREENWICH OFFICE PARK</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GREENWICH</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06831</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001385608</rptOwnerCik>
            <rptOwnerName>Southpaw Holdings LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>FOUR GREENWICH OFFICE PARK</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GREENWICH</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06831</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001385599</rptOwnerCik>
            <rptOwnerName>Wyman Kevin</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>FOUR GREENWICH OFFICE PARK</rptOwnerStreet1>
            <rptOwnerStreet2>FIRST FLOOR</rptOwnerStreet2>
            <rptOwnerCity>GREENWICH</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06831</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001385606</rptOwnerCik>
            <rptOwnerName>Golden Howard</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>FOUR GREENWICH OFFICE PARK</rptOwnerStreet1>
            <rptOwnerStreet2>FIRST FLOOR</rptOwnerStreet2>
            <rptOwnerCity>GREENWICH</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06831</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-12-18</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>U</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>4884508</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Pursuant to the Agreement and Plan of Merger (the &quot;Merger Agreement&quot;), dated as of August 20, 2009, by and among MediciNova, Inc. (&quot;MediciNova&quot;), Absolute Merger, Inc. and Avigen, Inc. (the &quot;Company&quot;), each share of the Company's common stock held by the reporting persons that was outstanding immediately prior to the effective time of the merger (the &quot;Effective Time&quot;) has been converted at the Effective Time into the right to receive convertible notes of MediciNova and one contingent payment right, as described in the Merger Agreement.</footnote>
        <footnote id="F2">The filing of this Form 4 shall not be construed as an admission that (i) Southpaw Credit Opportunity Master Fund LP (&quot;Fund&quot;), (ii) Southpaw Asset Management LP (&quot;Southpaw Management&quot;), (iii) Southpaw Holdings LLC (&quot;Southpaw Holdings&quot;), (iv) Kevin Wyman or (v) Howard Golden is or was for the purposes of Section 16(a) of the Securities Exchange Act of 1934, as amended, the beneficial owner of any of the shares of common stock of the Company's par value $0.001 per share (&quot;Common Stock&quot;) held by Fund. Pursuant to Rule 16a-1, Fund, Southpaw Management, Southpaw Holdings, Mr. Wyman and Mr. Golden disclaim such beneficial ownership beyond their pecuniary interest.</footnote>
        <footnote id="F3">Southpaw Management holds shares of Common Stock indirectly through the account of Fund, of which Southpaw Management serves as the investment manager. Southpaw Management or its affiliates receive a performance-based and an asset-based fee for managing the investments of Fund. Southpaw Holdings reports the shares of Common Stock held indirectly by Southpaw Management, because, as the general partner of Southpaw Management, it controlled the disposition and voting of the securities. Messrs. Wyman and Golden report the shares of Common Stock held indirectly by Southpaw Management because, as the managing members of Southpaw Holdings, they controlled the disposition and voting of the securities.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Kevin Wyman, managing member Southpaw GP, LLC, general partner, Southpaw Credit Opportunity Master Fund LP</signatureName>
        <signatureDate>2009-12-21</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Kevin Wyman, managing member, Southpaw Holdings LLC, general partner, Southpaw Asset Management LP</signatureName>
        <signatureDate>2009-12-21</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Kevin Wyman, managing member, Southpaw Holdings LLC</signatureName>
        <signatureDate>2009-12-21</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Kevin Wyman</signatureName>
        <signatureDate>2009-12-21</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Howard Golden</signatureName>
        <signatureDate>2009-12-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
