<SUBMISSION>
<ACCESSION-NUMBER>0001039160-05-000062
<TYPE>3
<PUBLIC-DOCUMENT-COUNT>1
<PERIOD>20041001
<FILING-DATE>20050809
<DATE-OF-FILING-DATE-CHANGE>20050809
<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>IVRI YEHUDA
<CIK>0001238778
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>3
<ACT>34
<FILE-NUMBER>000-31913
<FILM-NUMBER>051011320
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>4 TASMAN SEA
<CITY>NEWPORT COAST
<STATE>CA
<ZIP>92657
<PHONE>6508647300
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>2071 STIERLIN COURT
<CITY>MOUNTAIN VIEW
<STATE>CA
<ZIP>94043
</MAIL-ADDRESS>
</REPORTING-OWNER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>edgardoc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2004-10-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001238778</rptOwnerCik>
            <rptOwnerName>IVRI YEHUDA</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>2071 STIERLIN COURT, SUITE 100</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MT. VIEW</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94043</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Technical Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>33333</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>157500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by Trust</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.85</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2003-01-31</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2012-12-10</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>9000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.65</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-06-29</value>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-06-29</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>142360</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>15.05</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2002-06-30</value>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-12-12</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Non-Qualified Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.65</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-06-29</value>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-06-29</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>107640</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Shares held by the Yehuda &amp; Zipora Ivri Revocable Trust, in which Mr. Ivri has an economic interest.</footnote>
        <footnote id="F2">The option shall vest and become exercisable as to 9,000 shares divided into equal monthly installments beginning 12/31/02 such that it shall be 100% vested on 12/31/05.</footnote>
        <footnote id="F3">When the ISO and NQ dated 06/29/04 are combined for a total of 250,000 shares, they vest and become exercisable as to 62,500 shares on 06/29/05 then the balance of 187,500 shares shall be divided into equal monthly installments thereafter such that the option shall be 100% vested on 06/29/08</footnote>
        <footnote id="F4">The option shall vest and become exercisable as to 500 shares on 06/30/02, 12/31/02 and 06/30/03.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Yehuda Ivri</signatureName>
        <signatureDate>2005-08-10</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SUBMISSION>
