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?