The aim of this study was to investigate the effect of chronic microwave exposure on sperm count, sperm morphology, and the morphology of rat testis and epididymes. Continuous wave microwave radiation (9450 MHz) specific absorption rate 1.80 W/kg and power density 2.65 mW/cm(2), was administered for 1 h a day for 13, 26, 39, and 52 days, which corresponded to 1, 2, 3, and 4 cycles of seminiferous epithelium, in mature male Sprague-Dawley rats. The rats were sacrificed under Ketalar anesthesia the day after exposure. Then epididymal sperm count, sperm morphology, and the weights of testis, epididymes, seminal vesicles, and prostate were determined. Histologic examinations of testis and epididymes were performed. The parameters were compared with sham groups. Epididymal sperm count decreased significantly only in the 52-day exposure group (p < 0.05). The percentage of abnormal sperm count changed significantly in the 26-, 39-, and 52-day exposure groups (p < 0.05, p < 0.05, and p < 0.001, respectively). The weights of testis and epididymes also changed significantly in the 26-, 39-, and 52-day exposure groups (p < 0.05, p < 0.05, and p < 0.05, respectively). Necrotic tubules, interstitial edema, perforated and necrotic tubules, decrease of spermatogenesis, and absent germinal epithelium in some tubules were observed in the exposed rat testes. In addition, we observed atrophy, interstitial edema, mononuclear cell infiltration, and increased fibroblastic activity in the exposed rat epididymes. We concluded that epididymal sperm count and morphology and weight and morphology of testis and epididymes were affected by chronic prolonged microwave exposure. The incidence of symptoms mentioned here depended on exposure duration.