This research was undertaken to determine the effects of the cyclophosphamide (CP) on the epididymal corpus 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 and 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 epididymal corpus, the mitochondria were significantly swollen or disrupted. The lumens of rough endoplasmic reticulum (rER) were also dilated and the number of secretory vesicles and lysosomes were increased respectively. CP caused changes in protein concentrations in the corpus of epididymis after CP treatment. Total proteins of 31 to 36 species were expressed in the corpus fluid. Then the more CP was increased, the more concentration of proteins caused to decrease, synthesize or increase in epididymal corpus. In contrast to the control group, in particular 88KD and the other 8 proteins in the corpus fluid, were decreased or disappeared respectively, whereas acid phosphatase and the other 9 proteins in the corpus fluid, were increased or synthesized respectively. The other proteins are not showed distinctive difference. It is suggested that treatment with CP alters the specific cell organelles and proteins in segment of the epididymal corpus.