A critical pre-cytotoxic and -apoptotic DNA lesion induced by methylating carcinogens and chemotherapeutic drugs is O6-methylguanine (O6MeG). The mechanism by which O6MeG causes cell death via apoptosis is only partially understood. The current model ascribes a role to DNA replication and mismatch repair, which converts O6MeG into a critical distal lesion (presumably a DNA double-strand break) that is finally responsible for genotoxicity and apoptosis. Here we analysed whether the PI3-like kinase ATM is involved in this process. ATM is a major player in recognizing and signaling DNA breaks, but most reports are limited to ionizing radiation. Comparing mouse ATM knockout fibroblasts (ATM-/-) with the corresponding wild-type (ATM+/+) we show that ATM-/- cells are hypersensitive to the cytotoxic and apoptosis-inducing effect of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Inhibition of O6-methylguanine-DNA methyltransferase (MGMT) activity by O6-benzylguanine enhanced cell killing whereas the increase of MGMT activity by transfection with an expression vector provoked MNNG resistance. This was more pronounced in ATM-/- than in ATM+/+ cells, suggesting that O6MeG is responsible, at least in part, for increased MNNG sensitivity of ATM-/- cells. Cytogenetic studies showed that MNNG-induced sister-chromatid exchange frequencies were the same in ATM-/- and ATM+/+ cells in the first mitoses following treatment, but higher in ATM-/- cells than in the wild-type in the second post-treatment mitoses, when MGMT was depleted. Also, a significant higher frequency of MNNG-induced chromosomal aberrations was observed in ATM-/- than in ATM+/+ cells when analysed at a late recovery time, which is consistent with O6MeG being the inducing lesion. In summary, we conclude that ATM is not only involved in resistance to ionizing radiation but also to methylating agents, playing a role in the repair of secondary DNA damage generated from O6MeG lesions. The data also show that ATM is not required for activating the apoptotic pathway in response to O6MeG since ATM-/- cells are able to undergo apoptosis with high frequency.