Collaboration plays an increasingly important role in promoting research productivity and impact. What remains unclear is whether female and male researchers in science, technology, engineering, and mathematical (STEM) disciplines differ in their collaboration propensity. Here, we report on an empirical analysis of the complete publication records of 3,980 faculty members in six STEM disciplines at select U.S. research universities. We find that female faculty have significantly fewer distinct co-authors over their careers than males, but that this difference can be fully accounted for by females’ lower publication rate and shorter career lengths. Next, we find that female scientists have a lower probability of repeating previous co-authors than males, an intriguing result because prior research shows that teams involving new collaborations produce work with higher impact. Finally, we find evidence for gender segregation in some sub-disciplines in molecular biology, in particular in genomics where we find female faculty to be clearly under-represented.