In the most recent episode of the show Agents of S.H.I.E.L.D., "Girl in the Flower Dress", it is revealed that S.H.I.E.L.D. has a "short list" of individuals with various powers, such as the man in China with pyrokinetic abilities.
However, given that the show is supposed to tie into the larger cinematic universe, is S.H.I.E.L.D. aware of the existence of the X-Men, or are the Avengers and X-Men films/franchises intended to be seen as completely separate film universes for Marvel?
Marvel licensed the Mutants portion of their universe to Fox. This means the marvel-cinematic-universe has no mutants in it*, as they can't use those characters. Ergo, in Agents of S.H.I.E.L.D. there are no mutants, which means no X-Men, no Brotherhood of Evil Mutants, etc.
*The exception being Scarlet Witch and Quicksilver, which are a special part of the license deal. Fox can use them as mutants and children of Magneto. Marvel can use them as Avengers, but can't mention their mutant status or mention Magneto.
Currently Marvel doesn't have rights for X-men, Spider-man and Fantastic Four (or might be few more guys). So in the Marvel Cinematic Universe, they can't mention any mutant (X-men) till they got permission from Fox, which doesn't seems possible for now as Fox isn't going to share the mutants with Marvel.
With one exception that Marvel has rights to a few X-men characters like Quicksilver, Scarlet Witch and few more but without mentioning their mutant or X-men connection. So we can assume that X-men belongs to different a universe then Marvel Cinematic Universe.
Even Tancharoen said that "We can't ever say 'mutant'" (Source: MTV.com news).
