Background: Cimetidine, an H2 receptor antagonist, has been shown to be clinically valuable in the treatment of peptic ulcers. Recently, the effect of cimetidine on the reproductive system has been studied in detail and there are some reports showing the untoward effects of cimetidineon this system. We have previously reported that, cimetidine treatment decreased sperm count and motility in rats. The present study was undertaken to evaluate the effect of cimetidine on serum testosterone, testes, prostate, seminal vesicle and vas deferens. Apart from the above objective, the mechanism through which cimetidine can affect sperm motility and count was also sought. Materials and Methods: Eighty male rats were divided into 8 Groups: Group 1 (control) received no treatment, Group 2 (sham) received normal saline for 5 weeks and the experimental groups received 100 mg/kg of body weight of cimetidine for 1 week (Group 3), 2 weeks (Group 4), 3 weeks (Group5), 4 weeks (Group 6) and 5 weeks (Groups 7 and 8). However, to evaluate the reversible effects of cimetidine, Group 8 did not receive any treatment on week 6. Serum testosterone was measured before the experiment, one day after the first injection, and thereafter once every three days throughout the experiment. At the end of the experiment, testes, prostate and seminal vesicle were removed and weighed. These organs as well as the vas deferenses were prepared for the histopathologic staining and evaluation. Results: The results showed that serum testosterone and the weight of testes and prostate and their ratios to body weight were unchanged after cimetidine treatment. However, the weight of the seminal vesicle and its ratio to body weight were significantly decreased after 5 weeks of treatment, although these changes were reversible one week after termination of treatment. Conclusion: It seems that cimetidine might have a direct effect on the seminal vesicle probably by decreasing its zinc content. The results suggest that, the effects of cimetidine on sperm count and motility is either direct or through a change in the seminal vesicle secretary machanism.