The increasing use of pesticides in modern agriculture has raised the need to evaluate their potential threat to animal and human health. In the present study, the genotoxic effects of environmentally relevant exposure to the fungicide thiophanate-methyl (TM) were assessed in the lizard Podarcis sicula (Reptilia, Lacertidae) using micronucleus test, chromosome aberration analysis and single-cell gel electrophoresis (comet) assay. The number of micronuclei increased significantly with exposure time in lizard specimens exposed to 1.5% TM for 30–40 days. In situ hybridization with the specific HindIII centromeric satellite was positive in 18.7% of the micronuclei observed, suggesting an aneugenic effect of TM during mitosis. DNA damage, evaluated by the comet assay, documented a significant gain in comet length in relation to exposure time that was paralleled by a reduction in head size. Finally, cytogenetic analysis showed a significant increase in chromosome aberrations in exposed animals compared with controls. Our data suggest that long-term TM exposure induces a genomic damage that is positively correlated to exposure time. If such genotoxic effects arise so clearly in an ectothermal vertebrate, such as P. sicula, prolonged exposure TM must be considered as a cytogenetic hazard.