Phytoestrogens are plant-derived compounds with oestrogenic activity. They are common in both human and animal diets, particularly through soy-based foods. This study assessed whether exposure of adult male rats to a high phytoestrogen diet for 3-25 days affected their fertility, and assessed possible mechanisms through which phytoestrogens may disrupt fertility. Adult males, fed a high phytoestrogen diet for 3 days, demonstrated significantly reduced fecundity. This effect was transient, with fecundity returning to control levels by day 12. The expression of oestrogen receptor-alpha and androgen receptor mRNA was increased in the initial segment of the epididymis, but decreased in the cauda epididymis following 3 days on the high phytoestrogen diet. Epididymal sperm counts cannot account for the reduction in fertility at day 3. However, lipid peroxidation of epididymal sperm was significantly increased in animals fed a high phytoestrogen diet for 3 days. Disruption of the steroid regulation of the epididymis by phytoestrogens may alter its function, resulting in decreased quality of sperm, and thereby reducing fecundity.