Whether to be male or female is a critical decision in development. Nowhere is this more important than in the germ cells, which must produce either the sperm or eggs necessary for the perpetuation of the species. How does a germ cell make this decision and how is it executed? One thing that is clear is that this process is very different in germ cells compared with other cells of the embryo. Here, we explore how sexual identity is established in the Drosophila germline, how this affects other aspects of germ cell development and what studies in Drosophila can teach us about mammalian germ cells.