The effects of the mutagens, cyclophosphamide (CP), ethyl methanesulphonate (EMS), bleomycin (BLM) and the testicular toxin ethylene glycol monomethyl ether (EGME) in bone marrow and testicular cells have been compared in the alkaline COMET assay. Sprague-Dawley rats were administered by gavage with 50, 100 and 150 mg/kg body weight (bw) of CP; 100, 200 and 300 mg/kg bw EMS; 50, 100 and 150 mg/kg bw BLM and 500, 1000 and 1500 mg/kg bw EGME. Effects were examined at week 2 after treatment for CP, EMS BLM and EGME and at weeks 5 and 6 for EGME. Bone marrow cells were removed and separated by aspiration of the femur and testicular cells by decapsulation of the testis, treating with collagenase followed by trypsin. Various statistical methods were used to analyse the data. For CP there was an increase in damage above control values for bone marrow at 50 mg/kg bw which decreased at 100 mg/kg bw, and there was mortality of the animals at 150 mg/kg bw. A similar response was found in the testicular cells. For EMS and BLM, there were only occasional slight increases in damage in bone marrow and testicular cells. Two studies were conducted with EGME. In the first, where effects were examined at week 2 after treatment, there was an increase in damage in bone marrow cells, but a larger response was observed in testicular cells. In the second study where effects were examined at weeks 5 and 6 after treatment, bone marrow and testicular cells were not affected. The overall results showed that damage persisted for 2 weeks after treatment with CP and EGME but not in weeks 5 and 6 for EGME. Various statistical methods were used to analyse the data. Statistically significant responses were produced after treatment with CP and EGME and were dose-related for EGME, but after treatment with EMS and BLM statistical increases were sporadic. These results suggest that the assay is useful for measuring DNA damage and its persistence, and for comparing the sensitivity of different target organs in vivo.