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My real question is how are patches and updates authenticated in general. But for example how does windows know a windows update is really a windows update, does it just trust the URL or is there some kind of certificate?

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All updates are digitally signed by Microsoft's private key, you will get warnings if any updates are not signed, or signed with the wrong key. Even if a MiTM was able to send fake updates they'd be rejected by the update utility for that reason.

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Comodohacker, the guy who breached DigiNotar last year, claimed that he is able to issue fake certificates in the identity of Microsoft, and that he could provide fake updates. http://news.cnet.com/8301-1009_3-20104883-83/comodohacker-i-can-issue-fake-windows-updates/ I haven't heard any confirmation of this happening, and Microsoft moved immediately to revoke the trust of DigiNotar as soon as the hack was announced, so it's possible nothing happened as a result.

But my advice is you are still much safer trusting it than you are to run un-patched; just don't be completely surprised if someone does breach it some day.

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