Purpose: Phytoestrogens are oestrogens that are non-steroidal and are naturally found in plants. This study examined the effects of a phytoestrogen-containing diet on the thin layer of epididymis at electron microscopic level. Materials and Methods: This study was carried out to investigate the effects of a non-phytoestrogen diet (Phyto-0 group), a standard diet containing the same amount of phytoestrogen (Phyto-500 or control group), and a diet with a high dose of phytoestrogen (Phyto-1000 or phyto-rich group). Three different diets were prepared. Eighteen Swiss Albino type male mice 21 days old were obtained soon after weaning before they received any supplementary food and they were fed until they were 63 days old (9 weeks). For electron microscopy, tissue sections were processed and stained using the usual methods. Results: Basal cells and chief cells built-in in the basal epithelium of the epididymis were examined and found to have their normal structure in the Phyto-0 group. It was interesting that chief cells showed two different structural characteristics and basal cells preserved their general structure in the Phyto-500 group, while light and dark coloured chief cells and basal cells were examined and found to have diffuse degeneration in the Phyto-1000 group. Conclusion: Histological changes seen in the epididymis due to a high dose of phytoestrogen in the diet may cause infertility in male mice.