I have heard that female MIT undergraduates have been told by professors that they don't belong here and were only admitted through affirmative action. Not only is the statement unkind, but it is untrue. Women's grade point averages are the same as men's, even when adjusted for major, and they graduate at a higher rate. The situation doesn't necessarily get better after a woman has had the chance to prove herself. The same response greeted a woman I know when she got tenure.
Faculty members make eye contact with male students more often than with female students.
Faculty members are more likely to know and use the names of their male students than of female students. Women are often asked fewer or easier questions than men. While each isn't a big deal in and of itself, the cumulative effect of all this is to make a woman doubt herself. People have been talking about special programs to encourage women and minorities. I know of an extremely talented woman who left graduate school, on the advice of her advisor, because they both knew the sexist mistreatment she was receiving would continue.