Women are underrepresented in science and engineering, with the underrepresentation increasing in career stage. We analyze gender differences at critical junctures in the STEM pathway--graduate training and the early career--using UMETRICS administrative data matched to the 2010 Census and W-2s. We find strong gender separation in teams, although the effects of this are ambiguous. While no clear disadvantages exist in training environments, women earn 10% less than men once we include a wide range of controls, most notably field of study. This gap disappears once we control for women's marital status and presence of children.