Objective:To understand the mechanism of immunosuppression of cyclophosphamide. Methods: Investigate if cyclophosphamide produces the immunosuppression by the induction of apoptotic cell death in thymus .Results: 20 and 70 mg/kg cyclophosphamide could induce markedly apoptosis in rat thymus at 12 h after treatment ,the apoptotic cell death took place at 8~24 h and disappeared at 48 h after cyclophosphamide treatment. Conclusion: Cyclophosphamide may causes immunosuppression through the induction of apoposis of thymocyte.