The epididymis provides protection to sperm entering the epididymal duct against autoimmune damage, but in contrast must also protect itself against ascending pathogens This requires tolerance to sperm autoantigens in the caput involving anti-inflammatory intra-epithelial dendritic cells and macrophages (mononuclear phagocytes; MPs), however the cauda is much more susceptible to inflammatory damage. To better understand the basis for these regional differences, epididymal MP subsets were examined in immature (25 day-old, prior to mature sperm appearance) and sexually mature (56 day-old) mice possessing a fluorescent transgene inserted into gene loci of the MP-specific proteins, CX3CR1 (CX3CR1-GFP) or CD11c (CD11c-YFP). Tissues were fixed (4% paraformaldehyde), frozen-embedded in OCT and sectioned (10 μm). The pan-macrophage antigen, F4/80, was co-localised by indirect immunofluorescence. Sections were imaged by Olympus VSI 120 slide scanner and cells counted using Fiji software. The majority of intra-epithelial MPs were positive for F4/80, and CX3CR1 and/or CD11c at both days 25 and 56. These cells displayed extensive intra-epithelial cytoplasmic projections and were most abundant in the caput. Intra-epithelial projections were considerably less extensive in the adult corpus and cauda, and throughout the immature epididymis. F4/80+CX3CR1-, F4/80+CX3CR1+, F4/80+CD11c- and F4/80-CD11c+ macrophages with classical polygonal morphology were observed within all interstitial regions but were most prominent in the corpus and cauda at both ages. Interstitial F4/80+CX3CR1+ MPs were more numerous (2-3-fold) than F4/80+CX3CR1- MPs within the caput region, but approximately equal numbers of F4/80+CX3CR1- and F4/80+CX3CR1+ MPs were present within the cauda interstitium. These major differences in number and distribution of MPs between caput and cauda suggest that the intra-epithelial F4/80+CX3CR1+ MPs predominant within the caput may contribute to the anti-inflammatory environment in that region. Conversely, the single positive F4/80+CX3CR1-, which are most abundant within the interstitium of the corpus and cauda, areas more susceptible to inflammation, may contribute to immune surveillance.