Male first instar larvae possess more germ cells in their gonads than female larvae of the same stage. To determine the earliest time point of sexual dimorphism in germ cell number, we have counted the germ cells of sexed embryos at different developmental stages. We found no difference in germ cell number of male and female embryos at the blastoderm and early gastrulation stage, or when germ cells are about to exit the midgut pocket. We find, however, that males have significantly more germ cells than females as soon as the germ cells are near the places where the gonads are formed and in all later stages. Our results show that germ cells are subject to a sex-specific control mechanism that regulates the number of germ cells already in embryos.