The present study investigated the radioprotective effect of a multifunctional soy isoflavone, genistein, with the testicular system. Genistein was administered (200 mg/kg body weight) to male C3H/HeN mice by subcutaneous injection 24 h prior to pelvic irradiation (5 Gy). Histopathological parameters were evaluated 12 h and 21 days post-irradiation. Genistein protected the germ cells from radiation-induced apoptosis (p < 0.05 vs vehicle-treated irradiated mice at 12 h post-irradiation). Genistein significantly attenuated radiation-induced reduction in testis weight, seminiferous tubular diameter, seminiferous epithelial depth and sperm head count in the testes (p < 0.05 vs vehicle-treated irradiated mice at 21 days post-irradiation). Repopulation and stem cell survival indices of the seminiferous tubules were increased in the genistein-treated group compared with the vehicle-treated irradiation group at 21 days post-irradiation (p < 0.01). The irradiation-mediated decrease in the sperm count and sperm mobility in the epididymis was counteracted by genistein (p < 0.01), but no effect on the frequency of abnormal sperm was evident. Reactive oxygen species (ROS) were evaluated using DCFDA method and exposure to irradiation elevated ROS levels in the testis and genistein treatment resulted in a significant attenuation of radiation-induced ROS production. The results indicate that genistein protects from testicular dysfunction induced by gamma-irradiation by an antiapoptotic effect and recovery of spermatogenesis.