Cyclophosphamide is a chemotherapeutical drug, with proved carcinogenic side effects. Our previous experiments showed its effect on the expression of certain oncogenes and tumor suppressor genes. In order to further explore the effects of cyclophosphamide at the gene level an in vivo mouse model was developed. We compared the effects of cyclophosphamide with that of cyclosporine, which is a non genotoxic human carcinogenic chemical. After different time periods of intraperitoneal cyclophosphamide or cyclosporine injection, RNA was isolated from whole organs of experimental animals, and expression of onco/suppressor genes was determined by slot blot hybridisation. In our model we have proved that gene expression changes caused by cyclophosphamide can be detected even six months after treatment without tumor development. Our results support the hypothesis that gene expression investigations could be useful biomarkers in monitoring the effects of environmental carcinogenic compounds.