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<ownershipDocument>

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    <periodOfReport>2006-03-16</periodOfReport>

    <issuer>
        <issuerCik>0001034088</issuerCik>
        <issuerName>ECLIPSYS CORP</issuerName>
        <issuerTradingSymbol>ECLP</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001175873</rptOwnerCik>
            <rptOwnerName>KELLY BRADEN R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>GENERAL ATLANTIC SERVICE COMPANY, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>220 HAMILTON AVENUE</rptOwnerStreet2>
            <rptOwnerCity>PALO ALTO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94301</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

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                <natureOfOwnership>
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                    <footnoteId id="F6"/>
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        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
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            <transactionDate>
                <value>2006-03-16</value>
            </transactionDate>
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                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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                </transactionShares>
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                    <value>23.75</value>
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                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See</value>
                    <footnoteId id="F7"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-03-16</value>
            </transactionDate>
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                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionAmounts>
                <transactionShares>
                    <value>11348</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>23.75</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
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    <footnotes>
        <footnote id="F1">By General Atlantic Partners 28, L.P. (&quot;GAP 28&quot;).  See footnote 9.</footnote>
        <footnote id="F2">By General Atlantic Partners 38, L.P. (&quot;GAP 38&quot;).  See footnote 9.</footnote>
        <footnote id="F3">By General Atlantic Partners 47, L.P. (&quot;GAP 47&quot;).  See footnote 9.</footnote>
        <footnote id="F4">By General Atlantic Partners 48, L.P. (&quot;GAP 48&quot;).  See footnote 9.</footnote>
        <footnote id="F5">By General Atlantic Partners 74, L.P. (&quot;GAP 74&quot;).  See footnote 9.</footnote>
        <footnote id="F6">By GapStar, LLC (&quot;GapStar&quot;).  See footnote 9.</footnote>
        <footnote id="F7">By GAP Coinvestment Partners, L.P. (&quot;GAPCO&quot;).  See footnote 9.</footnote>
        <footnote id="F8">By GAP Coinvestment Partners II, L.P. (&quot;GAPCO II&quot;).  See footnote 9.</footnote>
        <footnote id="F9">4,743,662 shares of common stock includes 644,893 shares owned by GAP 28, 2,272,000 shares owned by GAP 38, 309,179 shares owned by GAP 47, 247,431 shares owned by GAP 48, 483,174 shares owned by GAP 74, 36,758 shares owned by GapStar, 682,927 shares owned by GAPCO and 67,300 shares owned by GAPCO II.  General Atlantic LLC (&quot;GA LLC&quot;) is the general partner of GAP 28, GAP 38, GAP 47, GAP 48 and GAP 74.  GA LLC is also the sole member of GapStar.  The general partners of GAPCO and GAPCO II are Managing Directors of GA LLC.  Mr. Kelly is a Managing Director of GA LLC, and a general partner of GAPCO and GAPCO II.  Mr. Kelly disclaims beneficial ownership of such shares except to the extent of his pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Braden R. Kelly</signatureName>
        <signatureDate>2006-03-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
