The sociology of science has clearly established the presence of sex differences in scientific productivity and position. This article examines the processes leading to the lower productivity of female scientists at the completion of their doctoral training. Collaboration with the mentor is found to be the most important factor affecting productivity. For females, opportunities for collaboration are significantly decreased by having young children. As a consequence, the presence of young children has an adverse, indirect effect on the productivity of female scientists during graduate study. This effect does not exist for males. In addition to differences in the process of collaboration, many small differences that disadvantage women and advantage men are found in the levels of resources affecting productivity and in the mechanisms by which resources are translated into productivity. The concentration of small disadvantages provides a further explanation of sex differences in productivity at the start of the career. Since early advantages and disadvantages have been found to accumulate, this article provides an essential first step in understanding sex differences in scientific productivity and position that emerge during the career.