The POU domain is a approximately 140 amino acid domain shared by several mammalian transcriptional activators. We have isolated genomic and cDNA clones from three Drosophila POU domain genes, designated pdm-1, pdm-2, and Cf1a. All three genes encode a conserved POU-specific domain and a POU homeo domain but are otherwise divergent. By Northern analysis, all three of the genes are expressed in early embryos; the pdm-1 and Cf1a genes are also expressed at lower levels throughout development. The spatial expression patterns of the pdm-2 and Cf1a genes show that they probably play multiple roles during development: an early role in specific ectodermal cells, and a subsequent role in the embryonic nervous system.