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The epididymis plays an essential role in reproduction, promoting sperm cell maturation. In this study, we investigated the effects of a high-fat diet (HFD) in the three regions of the epididymis of rats, including caput, corpus, and cauda. Our results showed an increase in malondialdehyde and a decrease in superoxide dismutase, which indicated an increase in oxidative stress in all segments of the epididymis. The cellular response mechanisms were mostly detected in the corpus/ cauda regions, which showed an increase in apoptosis, probably for eliminating dysfunctional cells arising from HFD-induced oxidative stress, and a decrease in mitophagy. Additionally, an increase in lipophagy to prevent lipid accumulation and a decrease in cell proliferation were recorded in the corpus.