Cyclophosphamide (CP) has been reported to cause structural and numerical chromosome aberrations in mouse spermatocyte metaphase chromosomes. Further, it was concluded to be one of the few chemicals for which there appears to be reliable data suggesting that it can induce germ cell aneuploidy. In the present study, mice were injected with CP, and both prophase and metaphase analyses were conducted to better understand the qualitative and quantitative relationship between respective synaptonemal complex (SC) and chromosome endpoints. The intent was to confirm that CP induces aneuploidy and to assess what happens to the various types of SC damage as they may relate to aberrations observed at metaphase 1 and 2. In some instances, mice were injected with tritiated thymidine in addition to CP so that sequentially harvested prophase and metaphase cell samples could be accurately identified by autoradiography as belonging to the same treated cell population. The results substantiate SC analysis as a highly sensitive indicator of potentially heritable effects of this (and presumably other) genotoxic agents.