<SUBMISSION>
<ACCESSION-NUMBER>0000898432-05-000087
<TYPE>3/A
<PUBLIC-DOCUMENT-COUNT>1
<PERIOD>20050118
<FILING-DATE>20050201
<DATE-OF-FILING-DATE-CHANGE>20050201
<ISSUER>
<COMPANY-DATA>
<CONFORMED-NAME>AEROGEN INC
<CIK>0001039160
<ASSIGNED-SIC>3841
<IRS-NUMBER>330488580
<STATE-OF-INCORPORATION>DE
<FISCAL-YEAR-END>1231
</COMPANY-DATA>
<BUSINESS-ADDRESS>
<STREET1>2071 STIERLIN COURT
<CITY>MOUNTAIN VIEW
<STATE>CA
<ZIP>94043
<PHONE>650 864-7300
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>2071 STIERLIN COURT
<CITY>MOUNTAIN VIEW
<STATE>CA
<ZIP>94043
</MAIL-ADDRESS>
</ISSUER>
<REPORTING-OWNER>
<OWNER-DATA>
<CONFORMED-NAME>BIOTECHNOLOGY VALUE FUND L P
<CIK>0000918923
<ASSIGNED-SIC>6282
<STATE-OF-INCORPORATION>DE
<FISCAL-YEAR-END>1231
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>3/A
<ACT>34
<FILE-NUMBER>000-31913
<FILM-NUMBER>05567037
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>227 W MONROE STREET, SUITE 4800
<STREET2>227 W MONROE STREET, SUITE 4800
<CITY>CHICAGO
<STATE>IL
<ZIP>60606
<PHONE>415-288-23
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>227 W MONROE STREET, SUITE 4800
<STREET2>227 W MONROE STREET, SUITE 4800
<CITY>CHICAGO
<STATE>IL
<ZIP>60606
</MAIL-ADDRESS>
</REPORTING-OWNER>
<REPORTING-OWNER>
<OWNER-DATA>
<CONFORMED-NAME>BVF PARTNERS L P/IL
<CIK>0001055947
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>3/A
<ACT>34
<FILE-NUMBER>000-31913
<FILM-NUMBER>05567038
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>ONE SANSOME ST
<STREET2>39TH FL
<CITY>SAN FRANCISCO
<STATE>CA
<ZIP>94104
<PHONE>3122637777
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>227 W MONROE
<STREET2>SUITE 4800
<CITY>CHICAGO
<STATE>IL
<ZIP>60606
</MAIL-ADDRESS>
</REPORTING-OWNER>
<REPORTING-OWNER>
<OWNER-DATA>
<CONFORMED-NAME>BVF INC/IL
<CIK>0001056807
<FISCAL-YEAR-END>1231
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>3/A
<ACT>34
<FILE-NUMBER>000-31913
<FILM-NUMBER>05567034
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>ONE SANSOME ST
<STREET2>39TH FLOOR
<CITY>SAN FRANCISCO
<STATE>CA
<ZIP>94104
<PHONE>3122637777
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>C/O GROSVENOR CAPITAL MANAGEMENT
<STREET2>227 W MONROE ST, #4800
<CITY>CHICAGO
<STATE>IL
<ZIP>60606
</MAIL-ADDRESS>
</REPORTING-OWNER>
<REPORTING-OWNER>
<OWNER-DATA>
<CONFORMED-NAME>BIOTECHNOLOGY VALUE FUND II LP
<CIK>0001102444
<FISCAL-YEAR-END>1231
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>3/A
<ACT>34
<FILE-NUMBER>000-31913
<FILM-NUMBER>05567036
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>ONE SANSOME ST
<STREET2>39TH FL.
<CITY>SAN FRANCISCO
<STATE>CA
<ZIP>94104
<PHONE>3122637777
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>C/O GROSVENOR CAPITAL MANAGEMENT
<STREET2>227 W. MONROE ST #4800
<CITY>CHICAGO
<STATE>IL
<ZIP>60606
</MAIL-ADDRESS>
</REPORTING-OWNER>
<REPORTING-OWNER>
<OWNER-DATA>
<CONFORMED-NAME>BVF INVESTMENTS LLC
<CIK>0001132245
<STATE-OF-INCORPORATION>DE
<FISCAL-YEAR-END>1231
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>3/A
<ACT>34
<FILE-NUMBER>000-31913
<FILM-NUMBER>05567035
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>ONE SANSOME ST. 39TH FL
<CITY>SAN FRANCISCO
<STATE>CA
<ZIP>94104
<PHONE>3127392123
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>C/O GROSVENOR CAPITAL MANAGEMENT LP
<STREET2>227 W. MONROE ST. #4800
<CITY>CHICAGO
<STATE>IL
<ZIP>60606
</MAIL-ADDRESS>
</REPORTING-OWNER>
<DOCUMENT>
<TYPE>3/A
<SEQUENCE>1
<FILENAME>form3a_ex.xml
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2005-01-18</periodOfReport>

    <dateOfOriginalSubmission>2005-01-28</dateOfOriginalSubmission>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001039160</issuerCik>
        <issuerName>AEROGEN INC</issuerName>
        <issuerTradingSymbol>AEGN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001055947</rptOwnerCik>
            <rptOwnerName>BVF PARTNERS L P/IL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>227 WEST MONROE STREET</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 4800</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60606</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>Indirect Beneficial Owner</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000918923</rptOwnerCik>
            <rptOwnerName>BIOTECHNOLOGY VALUE FUND L P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>227 WEST MONROE STREET</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 4800</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60606</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See footnote (1)</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001102444</rptOwnerCik>
            <rptOwnerName>BIOTECHNOLOGY VALUE FUND II LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>227 WEST MONROE STREET</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 4800</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60606</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See footnote (1)</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001132245</rptOwnerCik>
            <rptOwnerName>BVF INVESTMENTS LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>227 WEST MONROE STREET</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 4800</rptOwnerStreet2>
            <rptOwnerCity>CHICAGO</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60606</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See footnote (1)</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001056807</rptOwnerCik>
            <rptOwnerName>BVF INC/IL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE SANSOME ST</rptOwnerStreet1>
            <rptOwnerStreet2>31ST FLOOR</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant No. 86</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-01-24</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-05-11</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>500000</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant No. 88</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-01-24</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-03-22</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>316663</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant No. 89</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-01-24</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-03-22</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>25014</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant No. 90</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-01-24</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-05-11</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1400</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant No. 91</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-01-24</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-03-22</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>339600</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant No. 92</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-01-24</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-05-11</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>400650</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares of Common Stock, par value $0.001 per share, underlying the Warrants reported in this response are directly
beneficially owned by Biotechnology Value Fund, L.P., a Delaware limited partnership (&quot;BVF, L.P.&quot;) (500,000 shares);
Biotechnology Value Fund II, L.P., a Delaware limited partnership (&quot;BVF2, L.P.&quot;) (316,663 shares); BVF Investments, L.L.C., a
Delaware limited liability company (&quot;Investments&quot;) (766,664 shares); and indirectly beneficially owned by BVF Partners L.P.,
a
Delaware limited partnership (&quot;Partners&quot;), and by its general partner (&quot;GP&quot;) BVF Inc., a Delaware corporation (&quot;BVF Inc.&quot;),
which is also an investment advisor to Partners. Partners is the general partner of BVF, L.P. and BVF2, L.P., and is the
manager of Investments.</footnote>
        <footnote id="F2">Pursuant to the operating agreement of Investments, Partners is authorized, among other things, to invest the funds of Ziff
Asset Management, L.P., the majority member of Investments, in the equity securities described herein as being beneficially
owned by Investments. Mark N. Lampert is the sole shareholder and sole director of BVF Inc., and is an officer of BVF Inc.
This joint filing on Form 3 shall not be deemed an admission that Mark N. Lampert is, for purposes of Section 16 of the
Securities Exchange Act of 1934, as amended, or otherwise, the beneficial owner of any equity securities covered by this
joint filing. Mr. Lampert disclaims beneficial ownership of shares reported in this response, except to the extent that he
has a pecuniary interest therein.</footnote>
        <footnote id="F3">Shares are directly beneficially owned by BVF, L.P.</footnote>
        <footnote id="F4">Shares are directly beneficially owned by BVF2, L.P.</footnote>
        <footnote id="F5">Shares are directly beneficially owned by Investments.</footnote>
        <footnote id="F6">The Warrants contain a cashless exercise provision.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>BVF Partners, L.P., By: BVF Inc., its GP, By: /s/ Mark N. Lampert, President</signatureName>
        <signatureDate>2005-02-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BIOTECHNOLOGY VALUE FUND, L.P., By: BVF Partners L.P., its GP, By: BVF Inc., its GP, By: /s/ Mark N. Lampert, President</signatureName>
        <signatureDate>2005-02-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BIOTECHNOLOGY VALUE FUND II, L.P., By: BVF Partners L.P., its GP, By: BVF Inc., its GP, By: /s/ Mark N. Lampert, President</signatureName>
        <signatureDate>2005-02-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BVF INVESTMENTS, L.L.C., By: BVF Partners L.P., its Manager, By: BVF Inc., its GP, By: /s/ Mark N. Lampert, President</signatureName>
        <signatureDate>2005-02-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>BVF Inc., By: /s/ Mark N. Lampert, President</signatureName>
        <signatureDate>2005-02-01</signatureDate>
    </ownerSignature>
</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SUBMISSION>
