A forthcoming research article (PDF) in the Proceedings of the National Academy of Sciences reports some pretty convincing evidence of gender bias even in the university science departments. Quoting from the abstract,
... In a randomized double-blind study (n = 127), science faculty from research-intensive universities rated the application materials of a student -- who was randomly assigned either a male or female name -- for a laboratory manager position. Faculty participants rated the male applicant as signiﬁcantly more competent and hireable than the (identical) female applicant. These participants also selected a higher starting salary and offered more career mentoring to the male applicant. The gender of the faculty participants did not affect responses, such that female and male faculty were equally likely to exhibit bias against the female student. ...
That is, 127 science faculty members were asked to evaluate the very same resume, the only difference being that on about half of them the name was male and on the others female, and those with male names received higher ratings, even from other women.
Kathleen Geier, in a blog post on the subject at The Washington Monthly's site, provides links to several other studies showing gender bias. She also reminds us that years ago Larry Summers wound up resigning as president of Harvard after suggesting that the underrepresentation of women in the sciences wasn't the result of bias but a consequence of different innate ability. (A quibble with Geier, who suggests that Summers is otherwise brilliant. If he were, he'd have given better economic advice to various governments.)
(Updated to include a link to Geier's blog post, omitted by mistake.)