This research was undertaken to determine the effects of the anticancer and immunosuppressive drug cyclophosphamide (CP) on the epididymal caput 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 20 mg/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 lumens of rough endoplasmic reticulum (rER) were also swollen, and the number of Golgi vesicles were increased, respectively. It is suggested that treatment with CP alters the specific cell organelles in the epididymis. CP caused changes in protein concentrations in caput of epididymis after CP treatment. Total proteins of 32 to 37 species such as lactate dehydrogenase, carnitine acetyltransferase and succinate dehydrogenase were expressed in the caput fluid. Then the more CP was increased, the more concentration of proteins caused to decrease, synthesize or increase in epididymis. In contrast to the control group, in particular carnitine acetyltransferase and the other 9 proteins in the caput fluid were decreased or disappeared, respectively, whereas lactate dehydrogenase and the other 5 proteins in the caput fluid were increased or synthesized, respectively. The other proteins are not showed distinctive difference. These alterations could be direct mediated by toxic effects of the drug on the epithelium or be secondary to changes in the spermatozoa as a result of the CP treatment.