Hepatocyte nuclear factor-3alpha (HNF-3alpha), a member of the hepatocyte-forkhead-homolog family of transcription factors, regulates gene expression in the endoderm-derived liver and lung. To determine if HNF-3alpha might also play a role in endodermal derivatives of the urogenital sinus, the expression of HNF-3alpha in male accessory sex organs was assessed by Northern blotting, in situ hybridization, and electrophoretic mobility shift analysis. RNA from the dorsolateral prostate (DP), ventral prostate (VP), anterior prostate (AP), seminal vesicle (SV), and bladder was compared with RNA from the liver and spleen as positive and negative controls, respectively. HNF-3alpha mRNA levels in the DP, VP, AP, and bladder were 20, 14, 5, and 6 times higher than the SV equivalent in the liver. HNF-3alpha mRNA was detected in 8 of 10 prostate epithelial cell lines (rat NRP 152 and 154, mouse Pr14, and human DU-145, PC3, LNCaP, ND-1, and BPH-1) but not in rat Dunning epithelial or mouse Pr12 cells. Addition of testosterone to castrated rats was found to prevent a drastic loss of HNF-3alpha mRNA in the VP. This result suggests that HNF-3alpha mRNA levels are at least indirectly regulated by testosterone. The HNF-3alpha mRNA is expressed in epithelial cells of the urogenital sinus derivatives VP, AP, DP, and bladder and Wolffian duct derivative, the SV. To confirm that functional HNF-3alpha protein is produced in the VP, electrophoretic mobility shift assays were performed with whole-cell extracts and high-affinity oligonucleotide (TTR-S) from the transthyretin promoter. Binding to TTR-S was disrupted when the extract was incubated with HNF-3alpha, but not with HNF-3beta, antibody. Taken together, the results using VP, AP, DP, SV, and bladder suggest that HNF-3alpha may play an important role in development and maintenance of urogenital tract epithelial cells.