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Is it possible to use enterprise search to figure out an individual user's permission in a web app? I would like to get all the root sites along with the sub-sites across all the site collections...

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The Membership web part should list off the sites they have access to. Have you checked that out? – David Lozzi May 24 '12 at 15:20
    
That has some limitations such as the user has to have contributor rights on a site for that to show up on the membership webpart. If the user is a site collection administrator or has full control over the site, the webpart doesn't pick up the site. – Emon May 25 '12 at 16:23
    
Ok. You might be able to use the search results web part, and filter the results out, not sure if you can get just the sites however. – David Lozzi May 25 '12 at 16:29

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