AbstractTreatment of the father with the anticancer alkylating agent cyclophosphamide has negative effects on embryonic development in the rat. Four‐week treatment of male rats with a low dose of cyclophosphamide cause a dramatic, dose‐dependent increase in postimplantation death of the progeny. Several recent studies have indicated that the paternal genome is required for the development of the extraembryonic tissues. Thus, the purpose of this study was to determine which tissues of the implanting embryo were affected by paternal exposure to cyclophosphamide. Male Sprague‐Dawley rats were given cyclophosphamide (6 mg/kg/day) or saline by gavage and bred to untreated female rats after 4 weeks of treatment. Pregnant female rats were killed on day 7 of gestation, and implantation sites were dissected from the uterus, fixed, embedded in Epon for semithin serial sectioning, and stained for subsequent light microscopy. Strikingly, many of the implantation sites of affected embryos sired by treated males displayed an apparently normal trophectoderm enclosing a region of dying cells, containing dark‐stained pyknotic nuclei. Very few or no inner cell mass‐derived embryonic cells were present in these implantation sites. Therefore, there is a selective death of inner cell mass‐derived cells in day 7 implantation sites obtained from the progeny of cyclophosphamide‐treated males. The results of this study suggest that treatment of the male with cyclophosphamide can affect paternal genes specifically required for development of the inner cell mass cells of the embryo, without an apparent effect on those genes required for normal