Cyclophosphamide is a widely used anticancer and immunosuppressive drug that affects fertility in men. In a previous study, we found that chronic, daily treatment of male rats with low doses of cyclophosphamide had no apparent effect on the pituitary-gonadal axis, whereas it had time- and dose-dependent effects on male reproductive organ weights, the hematologic system, and on pregnancy outcome. To determine whether cyclophosphamide induces morphological changes within the male reproductive system, a detailed qualitative and quantitative evaluation of changes in the histology of the testis and epididymis was undertaken. Adult male Sprague-Dawley rats were gavage-fed for 1, 3, 6, and 9 wk with saline (control), 5.1 (low dose) or 6.8 (high dose) mg/kg/day of cyclophosphamide; the testes and epididymides were prepared for light and electron microscopy. At the light microscopic level, the orderly process of spermatogenesis in the seminiferous tubules was not affected at any time point with either dose of the drug. A number of time-dependent drug-induced changes in the histology of the epididymis, however, were apparent: 1) an increase in the relative number and a change in the distribution of halo cells in the caput epididymidis, 2) an increase in the number and size of clear cells in the caput and/or cauda epididymidis, and 3) an increase in the size of clear cells in both the caput and cauda epididymides; these changes were time dependent. At the electron microscopic level, there was a dose-dependent, two- to threefold increase in the number of spermatozoa with abnormal flagellar midpieces in the lumen of both the caput and cauda epididymides. Although the 9 plus 2 axonemal complex and the 9 outer dense fibers were present and appeared normal, the close approximation of these two structures was lost in these abnormal spermatozoa. Such abnormal flagellar midpieces were also found in the testes of control and treated rats. Electron microscopic examination of the testis revealed that both Sertoli and Leydig cells were normal in appearance. The type and timing of the effects of cyclophosphamide on the histology of the testis and epididymis suggest that the drug could be affecting germ cells by 1) inducing changes in the developing spermatozoa in the testis, some of which are seen microscopically in the epididymal lumen, and/or 2) affecting epididymal morphology and function.