Methods that permit the sensitive detection of DNA damage and repair are of special significance in the field of environmental research due to the long latent period between exposure to environmental agent(s) and genetic effect(s) becoming apparent. Malathion is a commonly used organophosphorus insecticide reported to be genotoxic both in vivo and in vitro, but the reports are conflicting. In order to elucidate the genotoxic potency of a compound present in commercial preparations of malathion, the DNA damaging effect of the insecticide and its isomer isomalathion was investigated using alkaline single cell gel electrophoresis (comet assay). Freshly isolated human peripheral blood lymphocytes were incubated with 75 and 200 µM of the chemicals for 1 h. The concentrations from the range we used, is relevant to that in blood following various nonlethal human exposure to pesticides. Malathion did not cause any significant changes in the comet length of the lymphocytes throughout the range of concentrations tested. Isomalathion introduced damage to DNA in a dose-dependent manner. Treated cells were able to recover within the 60 min incubation in insecticide-free medium at 37°C. The reported genotoxicity of malathion might, therefore, be a consequence of its thermal and/or photochemical conversion to isomalathion and the presence of isomalathion as well as its oxidation products and other unspecified impurities in commercial formulations of malathion. In this regard, the results of our study indicate that malathion used as commercial product, i. e. containing isomalathion, can be considered as a genotoxic substance in vitro. This means that it can produce DNA disturbances in vivo. Therefore, malathion can be regarded as a potential mutagen/carcinogen and requires further investigation.