Cyclophosphamide (CY) is an alkylating agent used in chemotherapy of tumors and autoimmune disorders. The drug causes a large number of side-effects including deep, transient lymphopenia and neutropenia, thus rendering the immune system susceptible to infections. In this review we focus on the effects of CY on the haematopoetic system and the immune response in rodents. In addition, we present approaches aimed at reconstitution of lympho- and myelopoiesis using a spectrum of immunotropic factors including: thymic hormones, cytokines, low-molecular weight compounds, bacterial products and lactoferrin.