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Eric Enge: If Googlebot sees an affiliate link out there, does it treat that link as an endorsement or an ad?
Matt Cutts: Typically, we want to handle those sorts of links appropriately. A lot of the time, that means that the link is essentially driving people for money, so we usually would not count those as an endorsement.
Eric Enge: If people do have ads on your site, it's still Google's wish that people NoFollow those links, correct?
Matt Cutts: Yes, absolutely. Our philosophy has not changed, and I don't expect it to change. If you are buying an ad, that's great for users, but we don't want advertisements to affect search engine rankings.
Should we find another way of "hiding" the links or does Google just recognize that it is an affiliate link?
So it would seem that there is no clear agreement on this! Matt Cutts comment to me implies that Google recognises an affiliate link and will treat it as such anyway (whether or not it is a well known affiliate) so what is the point of nofollowing the links, other than to perhaps show Google that you as the webmaster is being honest to them that it is an affiliate link?