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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2010-12-17</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001030574</rptOwnerCik>
            <rptOwnerName>FIDELMAN BARRY J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ATLAS VENTURE</rptOwnerStreet1>
            <rptOwnerStreet2>25 FIRST STREET, SUITE 303</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02141</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2010-12-17</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2010-12-17</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>U</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>12817090</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>33.85</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Includes 12,648,444 shares held by Atlas Venture Fund V, L.P., and 168,646 shares held by Atlas Venture Entrepreneurs' Fund V, L.P.  Atlas Venture Associates V, L.P. is the general partner of Atlas Venture Fund V, L.P. and Atlas Venture Entrepreneurs' Fund V, L.P.   Each of the Filing Persons disclaims beneficial ownership of such shares except to the extent of its pecuniary interest therein.  Mr. Fidelman disclaims beneficial ownership of the shares except to the extent of his pecuniary interest therein.  Mr. Fidelman is a director of Issuer</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Barry J. Fidelman, By Kristen Laguerre, as attorney-in-fact</signatureName>
        <signatureDate>2010-12-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
