Hox genes determine the formation of segmented structures during development. The epididymis shows a segmented organization in its structure and function beyond embryogenesis. This study examined the adult mouse epididymis and vas deferens for expression of 5′ hox genes and a hox-DNA binding cofactor. Reverse transcriptase-polymerase chain reaction (RT-PCR) showed the expression of hoxa-9, hoxa-10, hoxa-11, hoxd-9, and hoxd-10 in all regions including the vas deferens. Semiquantitative RT-PCR revealed highest mRNA levels for hoxa-11 in the distal part of the epididymis and vas deferens, and this was confirmed by Northern blot analysis. To determine protein presence an antibody raised against a peptide N-terminal to the homeodomain of hoxa-11 was produced in rabbits. The antibody recognized a band of approximately 37–39 kDa in Western blot analysis. Immunohistochemistry indicated the presence of hoxa-11 in the nuclei of the epithelial cells with some staining in the cytoplasm. Staining was also detected in nuclei of interstitial cells throughout the entire organ and the vas deferens. A DNA binding cofactor for hoxa-11, Meis 1, was investigated for its presence in the epididymis. Semiquantitative RT-PCR identified both transcripts for Meis 1 (Meis 1a and Meis 1b) in all regions. Protein presence was confirmed by Western blot analysis, and this detected one band of approximately 53–55 kDa. Immunohistochemistry localized Meis 1 in the nuclei of interstitial cells throughout the entire organ and the vas deferens. Our study provides preliminary data from which we suggest the involvement of homeodomain transcription factors in the maintenance of segmental function of the adult epididymis and vas deferens.