Hibiscus rosa-sinensis Linn. is one of medicinal plants in Indonesia that is used as a male contraceptive. Hibiscus flower contains flavonoids that can decrease testosterone. The purpose of this study was to determine the effects of hibiscus flower extract on the weight of the epididymis, prostate and seminal vesicles, and the thickness of the cauda epididymal epithelium, in male rats. 25 male Sprague Dawley® rats aged 60-70 days and weighing 200-210 g were subdivided into 5 groups of 5 animals each, and were treated with 0 (control), 200, 300, 400, and 500 mg/kg body weight of hibiscus flower methanolic extract for 30 days. The results showed a decrease in weight of the epididymis in the treatment groups (P < 0.001). Also, there was also a decrease in the thickness of the cauda epididymial epithelium (P = 0.021), as well as the weight of the prostate and seminal vesicles in treatment groups in comparison with the control group (P = 0.001). Therefore, hibiscus flower extract affected the weight of the epididymis, prostate and seminal vesicles and the thickness of cauda epididymial epithelium.