Communication among epididymal epithelial cells creates the best luminal condition where spermatozoa mature, transport and are stored. Vacuolar ATPase (V-ATPase) and cytokeratin 5 (KRT5) have been used as signal indicators for clear and basal cells of the epididymal epithelium, respectively, in mice, rats, bats, and pigs; however, these two markers have not yet been described in the epididymis of bulls. Here, we examined the presence and distribution of the B1 subunit of V-ATPase (B1-VATPase) and KRT5 in the distinct regions of adult bovine epididymides, specifically, the caput, corpus, and cauda. Immunofluorescence staining and confocal microscopy showed that narrow shaped-clear cells were placed in the caput and corpus regions of the bovine epididymis; however, they were absent in the cauda epididymis. In addition, B1-VATPase was highly expressed in the cauda spermatozoa; however, it was rarely detected in the caput spermatozoa. On the other hand, KRT5-positive cells, basal cells, were maintained beneath the basal lamina and they had the traditional form with a dome-shaped morphology from the caput to cauda region of the bovine epididymis. The co-expression of B1-VATPase and KRT5 was confined to basal cells placed in the basal region of the epithelium. In summary, 1) clear cells were present with region-specific localization, 2) B1-VATPase was present in the corpus and cauda spermatozoa but absent in the caput, 3) co-expressed cells with B1-VATPase and KRT5 were present in the adult bovine epididymis, and 4) B1-VATPase was not a specific marker for clear cells in the bovine epididymis. Therefore, the perfect epididymal luminal condition created by the specific expression and localization patterns of B1-VATPase might be necessary to obtain fertilizing capacity of spermatozoa in the bovine epididymis.