A complex situation of chemical exposure has been described in México in a zone that is in transition from rural activities towards intensive industrialization, which has brought environmental pollution: chloroform, methylene chloride, indigo and toluene are some of the pollutants found in the Atoyac and Xochiac rivers. A biomonitoring study was planned in order to establish whether there was a biological effect due to the environmental situation. Communities where leukaemia and thrombocytopenic purpura cases have been reported were included in the study, as well as other communities where such cases have not been described. Three occupations were distinguished, according to chemical exposure: industrial workers, agricultural workers and workers in households, education and commerce. A comprehensive analysis in the micronucleus (MN) test was used to study genotoxicity biomarkers. Two metabolic polymorphisms were determined, namely, glutathione transferase mu1 (GSTM1) and theta1 (GSTT1), which are relevant when oxidative responses are involved. Increased genotoxic damage was found, including cells with >1 MN, >1 chromatin bud, and nucleoplasmic bridges. The genotoxic damage was differentially distributed in the regions studied, being more affected those that are closer to the Atoyac and Xochiac rivers, indicating an effect due to environmental exposure to the contaminants present in the rivers. Further characterization of the exposure regimes in these communities will be done in order to contribute to the alleviation of the health risks that environmental pollution is posing on the inhabitants of this area.