In adult animals, spermatogenesis involves a continuous differentiation of the spermatogonial stem and progenitor cell population into mature sperm. A unique aspect of this developmental process is the germ cell-specific expression and function of paralogues of components of the general transcription machinery, notably subunits of TFIID. Genetic and biochemical studies show that these paralogues play critical, but mechanistically distinct roles in Drosophila and mouse spermatogenesis.