The molecular mechanisms involved in growth and morphogenesis of the mammalian urogenital system are largely undefined. In this study, we describe the cloning and characterization of a novel murine homeobox gene, Nkx3.1, which is expressed in the male urogenital system during late embryogenesis and adulthood. We show that Nkx3.1 encodes a 38 kDa homeoprotein that has DNA binding properties similar to those of other Nkx family members. By RNAse protection analysis, we demonstrate that Nkx3.1 is expressed in late-gestation embryos and adults by tissues of the male urogenital system, including the testis, seminal vesicle, and the prostate. In adult males, expression of Nkx3.1 in the prostate increases during sexual maturation, and is significantly reduced following castration, suggesting that androgens are required for maintenance of Nkx3.1 expression. In situ hybridization analysis of mid- and late-gestation male embryos shows that Nkx3.1 is expressed in the developing urogenital sinus, testis, and prostatic buds. In addition to its expression in the urogenital system, we also find that Nkx3.1 is expressed in the dorsal aorta and kidney. These results implicate Nkx3.1 in the growth and development of the prostate and/or other tissues of the male urogenital system, and suggest that Nkx3.1 may play a role in sexually dimorphic as well as non-sexually dimorphic organogenesis.