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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-02-24</periodOfReport>

    <notSubjectToSection16>false</notSubjectToSection16>

    <issuer>
        <issuerCik>0001373671</issuerCik>
        <issuerName>Isilon Systems, Inc.</issuerName>
        <issuerTradingSymbol>ISLN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001381752</rptOwnerCik>
            <rptOwnerName>McIlwain Matthew S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O MADRONA VENTURE GROUP, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>1000 SECOND AVE., STE. 3700</rptOwnerStreet2>
            <rptOwnerCity>SEATTLE</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>true</isDirector>
            <isOfficer>false</isOfficer>
            <isTenPercentOwner>true</isTenPercentOwner>
            <isOther>false</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>31750</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-02-24</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>30000</value>
                    <footnoteId id="F2"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.0878</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>8539117</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-02-25</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>75024</value>
                    <footnoteId id="F4"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.0953</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>8614141</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">4,000 shares were acquired through reporting person's 401k plan.</footnote>
        <footnote id="F2">Reflects a weighted-average price.  These shares were purchased in multiple transactions at prices ranging from $2.00 to $2.14, inclusive.  For all transactions reported in this Form 4 utilizing a weighted-average price, the reporting person will provide to the issuer, any security holder of the issuer, or the SEC staff, upon request, information regarding the number of shares sold at each price within the range.</footnote>
        <footnote id="F3">Represents 6,885,024 shares held by Madrona Venture Fund I-A, LP, 749,353 shares held by Madrona Venture Fund I-B, LP and 904,740 shares held by Madrona Managing Director Fund, LLC. Madrona Investment Partners, LLC is the general partner of Madrona Venture Fund I-A, LP and Madrona Venture Fund I-B, LP and disclaims beneficial ownership of the shares except to the extent of its pecuniary interest therein.  Mr. McIlwain is a managing director and member of various entities affiliated with Madrona Venture Group, LLC. Mr. McIlwain does not have sole voting or dispositive authority over these shares and disclaims beneficial ownership of these shares except to the extent of his pecuniary interest therein.</footnote>
        <footnote id="F4">Reflects a weighted-average price. These shares were purchased in multiple transactions at prices ranging from $2.01 to $2.15, inclusive. For all transactions reported in this Form 4 utilizing a weighted-average price, the reporting person will provide to the issuer, any security holder of the issuer, or the SEC staff, upon request, information regarding the number of shares sold at each price within the range.</footnote>
        <footnote id="F5">Represents 6,945,516 shares held by Madrona Venture Fund I-A, LP, 755,936 shares held by Madrona Venture Fund I-B, LP and 912,689 shares held by Madrona Managing Director Fund,  LLC.  Madrona Investment Partners, LLC is the general partner of Madrona Venture Fund I-A, LP and Madrona Venture Fund I-B, LP and disclaims beneficial ownership of the shares except to the extent of its pecuniary interest therein.  Mr. McIlwain is a managing director and member of various entities affiliated with Madrona Venture Group, LLC. Mr. McIlwain does not have sole voting or dispositive authority over these shares and disclaims beneficial ownership of these shares except to the extent of his pecuniary interest therein.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Keenan Conder, Attorney-in-Fact</signatureName>
        <signatureDate>2009-02-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
