Cyclophosphamide(CTX) is one of the most effective cytotoxic and immunosuppressive agent. It has many toxic side effects, including risk of secondary malignancy and myelosuppression. This compound has been shown to produce ovarian failure in humans and ovarian damage in animals treated for short or long time periods. In this study, the effects of cyclophosphamide (CTX) on the micronucleus frequency, urine and blood parameters, ovarian and uterine histology were investigated. 20 Sprague Dawley female cycling rats were divided into 2 groups: Group I(Control) was injected with 0.3ml/day physiologic saline (ip) . This injection was administered at the same time every day for a period 21 days. Group II(CTX) was injected (ip)with 50 mg/kg /day loading dose of CTX for the first two days of the experiment, then 5 ml/kg/day treatment dose of CTX for the remaining 19 days. As a result of the experiment, micronucleus frequency, SGOT and SGPT activities, creatinine clearance, urine creatinine, urea nitrogen, uric acid, urine volume, and pH levels increased in Group II, according to the control group. Histologically, a few of the primary follicle, and a large number of the corpus luteum were obtained in the ovaries, and decreasing gland and endometrium proliferation were determined in the uterine tissue of the group II animals.