Endocrine regulation of the mouse initial segment (IS) and distal caput epididymides was studied using genome-wide profiling of gene expression. Among the IS-enriched genes, 29% were significantly down-regulated 1 day after gonadectomy. Of those genes, dihydrotestosterone (DHT) supplementation was not sufficient to maintain their pregonadectomy level of expression in 70%. Of the caput-enriched genes, 16% were significantly down-regulated after gonadectomy, and of those genes, DHT supplementation did not maintain the initial level of expression in 28%. Identical data were obtained by clustering analyses performed for the expression data of epididymal genes. Furthermore, the microarray data revealed that 26 androgen receptor coregulators were expressed in the epididymis, of which several were confirmed by quantitative reverse transcriptase polymerase chain reaction analysis. This suggests putative involvement of these proteins in the segment-specific regulation of the epididymal genes. The pattern of epididymal gene expression in the novel proximal epididymis-specific androgen receptor knockout mouse ProxE-ARKO, with severe hypotrophy and hypoplasia of the caput epithelium, furthermore suggested that a subset of genes whose expression cannot be maintained by systemic androgen alone still require either direct lumicrine androgen action or a permissive effect of circulating testosterone. It is evident that testicular factors, one of which could be the high-concentration luminal androgen, are important for the expression of IS-enriched genes, whereas the expression of distal caput-enriched genes is typically regulated by systemic androgens.