This research was undertaken to determine the effects of the anticancer and immunosuppressive drug cyclophosphamide (CP) on the epididymis of the male rat in terms of ultrastructural alteration and protein analysis by SDS-PAGE at different groups; control group, 1 week group, 3 weeks group, 5 weeks group were treated with saline (control group) or CP at doses of 20mg/Kg/week, 1 time a week, respectively. In the cytoplasm of the principal cells on the epididymis, the mitochondrial outer and inner membranes were significantly swollen or disrupted. The cisterns of rough endoplasmic reticulum (rER) were also swollen, and a number of Golgi vesicles were increased, respectively. It is suggested that treatment with CP alters the specific cell organelles in all segments of the epididymis. CP caused changes in protein concentrations in cauda of epididymis after CP treatment. Total proteins of 30 to 39 species such as lactate dehydrogenase, carnitine acetyltransferase and acid phosphatase were expressed in the cauda fluid. Then the more CP was increased, the more concentration of proteins caused to decrease, synthesize or increase in epididymal cauda. In contrast to the control group, in particular 29KD and the other 10 proteins in the cauda fluid were decreased or disappeared, respectively, whereas 89KD and the other 6 proteins in the cauda, were increased or synthesized, respectively. The other proteins are not showed distinctive difference. Therefore, it is possible that CP at a high dose accumulation alters epididymal function with dose-related increase or decrease in specific activity of marked proteins for all regions of the epididymis (particularly, specific segment of cauda). These alterations could be mediated by direct, toxic effects of the drug on the epithelium or be secondary to changes in the spermatozoa as a result of the CP treatment.