Objective: The purpose of this study was to evaluate the effects of dietary phytoestrogens on mouse testis using light and electron microscopy and caspase-3 immunostaining. Materials and Methods: Eighteen male Swiss Albino mice of 3-weeks-old were separated into three groups, each including six mice, after weaning at postnatal 21st day. They were fed by three different diets; a phytoestrogen-free diet (phyto-0 group), a diet containing 500 μg/g phytoestrogen (phyto-500 group) or a diet containing 1000 μg/g phytoestrogen (phyto-1000 or phyto-rich group) for 6 weeks. After completing their sexual maturity on day 63, all were sacrificed under anesthesia. Extracted testes were prepared for investigation by light and electron microscopy and caspase-3 immunostaining was used to demonstrate the apoptosis. Results: During the study period, all mice in three dietary groups increased their weights regularly, but there was no statistically significant difference among groups for each week. Histological examination was normal in phyto-0 diet group by light and electron microscopy, and caspase-3 immunostaining showed no increased apoptosis. The phyto-500 and phyto-1000 diet caused a series of changes in the testis including increased apoptosis in the germ cells, increased edema in interstitial area, deposition of hyaline-like substance and increased lipid deposition in Leydig cells. These changes were more obvious in phyto-1000 group. The results of immunostaining by caspase-3 showed that apoptosis significantly increased in primary spermatocytes in both phyto-500 and phyto-1000 groups when compared to phyto-0 group (p=0.000). Discussion: Our results suggested that phytoestrogens might have detrimental effects on male reproductive function in a dose dependent manner.