<SUBMISSION>
<ACCESSION-NUMBER>0001005477-05-000077
<TYPE>3
<PUBLIC-DOCUMENT-COUNT>1
<PERIOD>20050103
<FILING-DATE>20050105
<DATE-OF-FILING-DATE-CHANGE>20050105
<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>XMARK ASSET MANAGEMENT LLC
<CIK>0001118481
<STATE-OF-INCORPORATION>NY
<FISCAL-YEAR-END>1231
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>3
<ACT>34
<FILE-NUMBER>000-31913
<FILM-NUMBER>05513439
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>CARNEGIE HALL TOWER
<STREET2>152 W 57TH ST 21ST FLOOR
<CITY>NEW YORK
<STATE>NY
<ZIP>10019
<PHONE>2122478200
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>CARNEGIE HALL TOWER
<STREET2>152 W 57TH ST 21ST FLOOR
<CITY>NEW YORK
<STATE>NY
<ZIP>10019
</MAIL-ADDRESS>
<FORMER-NAME>
<FORMER-CONFORMED-NAME>BROWN SIMPSON ASSET MANAGEMENT LLC
<DATE-CHANGED>20000707
</FORMER-NAME>
</REPORTING-OWNER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>edgar123.xml
<DESCRIPTION>FORM 3
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2005-01-03</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001118481</rptOwnerCik>
            <rptOwnerName>XMARK ASSET MANAGEMENT LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>152 W 57TH STREET, 21ST FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
                <footnoteId id="F5"/>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>53043</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A-1 Preferred Stock, par value $0.001 per share</value>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
                <footnoteId id="F5"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.00</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F7"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, par value $0.001 per share</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1666660</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant</value>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
                <footnoteId id="F5"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F8"/>
            </exerciseDate>
            <expirationDate>
                <value>2009-03-22</value>
                <footnoteId id="F9"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, par value $0.001 per share</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>764610</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant</value>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
                <footnoteId id="F5"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F10"/>
            </exerciseDate>
            <expirationDate>
                <value>2009-05-11</value>
                <footnoteId id="F11"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, par value $0.001 per share</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>902050</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Xmark Asset Management, LLC, a New York limited liability company (&quot;XAM&quot;), serves as investment manager for each of Xmark Fund, L.P., a Delaware limited partnership (&quot;Xmark LP&quot;), and Xmark Fund, Ltd., a Cayman Islands exempted company (&quot;Xmark Ltd&quot;).  In such capacity, XAM possesses the power to vote and direct the disposition of all securities held by Xmark LP and Xmark Ltd.  As of January 3, 2005, Xmark LP is the holder of (i) 74,025 shares (the &quot;Xmark LP Preferred&quot;) of the Series A-1 Preferred Stock, par value $0.001 per share (the &quot;Preferred Stock&quot;) of Aerogen, Inc., a Delaware corporation (the &quot;Company&quot;), which are presently convertible into 740,250 shares of the Company's common stock, par value $0.001 per share (the &quot;Common Stock&quot;), (ii) warrants expiring on March 22, 2009 which entitle Xmark LP to purchase up to an aggregate of 339,600 shares of Common Stock at an exercise price of $3.25 per share (the &quot;Xmark LP March 2009 Warrants&quot;),</footnote>
        <footnote id="F2">which exercise price is subject to adjustment as set forth in the Xmark LP March 2009 Warrants, (iii) warrants expiring on May 11, 2009 which entitle Xmark LP to purchase up to an aggregate of 400,650 shares of Common Stock at an exercise price of $3.25 per share (the &quot;Xmark LP May 2009 Warrants&quot;, and together with the Xmark LP March 2009 Warrants, the &quot;Xmark LP Warrants&quot;), which exercise price is subject to adjustment as set forth in the Xmark LP May 2009 Warrants and (iv) 23,560 shares of Common Stock issued in lieu of the cash payment of quarterly dividends on the Preferred Stock held by Xmark LP for the quarters ended March 31, June 30 and September 30, 2004.  Holders of Preferred Stock are entitled to receive dividends quarterly in arrears, in cash or Common Stock, at the Company's election, as more fully described in the Certificate of Designations, Preferences and Rights of the Company's Preferred Stock.</footnote>
        <footnote id="F3">As of January 3, 2005, Xmark Ltd is the holder of (i) 92,641 shares (the &quot;Xmark Ltd Preferred&quot;) of Preferred Stock, which are presently convertible into 926,410 shares of Common Stock, (ii) warrants expiring on March 22, 2009 which entitle Xmark Ltd to purchase up to an aggregate of 425,010 shares of Common Stock at an exercise price of $3.25 per share (the &quot;Xmark Ltd March 2009 Warrants&quot;), which exercise price is subject to adjustment as set forth in the Xmark Ltd March 2009 Warrants, (iii) warrants expiring on May 11, 2009 which entitle Xmark Ltd to purchase up to an aggregate of 501,400 shares of Common Stock at an exercise price of $3.25 per share (the &quot;Xmark Ltd May 2009 Warrants&quot;, and together with the Xmark Ltd March 2009 Warrants, the &quot;Xmark Ltd Warrants&quot;), which exercise price is subject to adjustment as set forth in the Xmark Ltd May 2009 Warrants</footnote>
        <footnote id="F4">and (iv) 29,483 shares of Common Stock issued in lieu of the cash payment of quarterly dividends on the Preferred Stock held by Xmark Ltd for the quarters ended March 31, June 30 and September 30, 2004.  The terms of the Xmark LP Preferred, the Xmark Ltd Preferred, the Xmark LP Warrants and the Xmark Ltd Warrants originally precluded each of Xmark LP and Xmark Ltd from converting the Xmark LP Preferred and the Xmark Ltd Preferred or exercising the Xmark LP Warrants and the Xmark Ltd Warrants if the conversion or exercise would result in Xmark LP, Xmark Ltd and/or their affiliates beneficially owning in excess of 4.99% of the Company's outstanding Common Stock following the conversion or exercise (the &quot;Issuance Limitation&quot;).  Each such Issuance Limitation was waiveable by Xmark LP and Xmark Ltd, respectively, providing 61 days' advance written notice to the Company.</footnote>
        <footnote id="F5">On November 3, 2004, Xmark Fund, LP and Xmark Fund, Ltd each provided a written waiver of the Issuance Limitation to the Company.  As a result of this waiver and as a result of the fact that XAM possesses the sole power to vote and direct the disposition of the securities described above, for purposes of Reg. Section 240.13d-3, XAM may be deemed to beneficially own 3,386,363 shares of Common Stock, or approximately 41.2% of the shares of Common Stock deemed issued and outstanding as of January 3, 2005.  XAM's interest in the securities reported herein is limited to its pecuniary interest in Xmark LP and Xmark Ltd, if any.  Mitchell D. Kaye is Chief Investment Officer of XAM, and as such possesses sole power to vote and direct the disposition of all securities of the Company held by Xmark LP and Xmark Ltd.</footnote>
        <footnote id="F6">The Preferred Stock is immediately convertible.</footnote>
        <footnote id="F7">The Preferred Stock has no expiration date.</footnote>
        <footnote id="F8">The Xmark LP March 2009 Warrants and the Xmark Ltd March 2009 Warrants are immediately exercisable.</footnote>
        <footnote id="F9">The Xmark LP March 2009 Warrants and the Xmark Ltd March 2009 Warrants expire on March 22, 2009, unless the expiration date is extended as more fully detailed in the Xmark LP March 2009 Warrants and the Xmark Ltd March 2009 Warrants, respectively.</footnote>
        <footnote id="F10">The Xmark LP May 2009 Warrants and the Xmark Ltd May 2009 Warrants are immediately exercisable.</footnote>
        <footnote id="F11">The Xmark LP May 2009 Warrants and the Xmark Ltd May 2009 Warrants expire on May 11, 2009, unless the expiration date is extended as more fully detailed in the Xmark LP May 2009 Warrants and the Xmark Ltd May 2009 Warrants, respectively.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Mitchell D. Kaye, Manager of Xmark Asset Management, LLC</signatureName>
        <signatureDate>2005-01-05</signatureDate>
    </ownerSignature>
</ownershipDocument>

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