We have shown previously that a network of mononuclear phagocytes (MPs) expressing macrophage and dendritic cell markers such as CD11c, F4/80 and CX3CR1, lines the base of the epididymal tubule. However, in the initial segment (IS) and only in that particular segment, epididymal MPs establish extremely close interactions with the epithelium by projecting slender dendrites between most epithelial cells. We undertook the present study to determine how epididymal phagocytes respond to the transient wave of apoptosis initiated by unilateral efferent duct ligation (EDL) in the epididymal epithelium. We show profound morphological and phenotypical changes restricted to the MPs populating the proximal epididymis following EDL. Within 48 h, a large subset of IS epithelial cells had entered an apoptotic state, visualized by the terminal deoxynucleotidyl transferase dUTP nick end labelling (TUNEL) assay and CD11c(+) and CX3CR1(+) MPs readily engulfed TUNEL-positive cells and other debris. Despite the high levels of apoptosis and the rapid clearance of apoptotic cells occurring after EDL, the epithelium preserved its overall architecture and maintained tight junctions of the blood-epididymis barrier (BEB). The discovery of a functional population of MPs in the epididymal epithelium responsible for maintaining the integrity of the BEB raises further questions regarding the role of these cells in clearing defective epithelial cells in the steady-state epididymis, as well as pathogens and abnormal spermatozoa in the lumen.