Inorganic arsenic (i-As) is an environmental carcinogen to which millions of people are chronically exposed mainly via drinking water. In this study, we used the comet assay to evaluate DNA damage in i-As-exposed inhabitants of the north of Mexico. The environmental monitoring and the exposure assessment were done by measuring both drinking water arsenic (As) content and total urinary As. In addition, the studied population was genetically characterized for four different glutathione S-transferase omega1 (GSTO1) polymorphisms (Ala140Asp, Glu155del, Glu208Lys, and Ala236Val) and the As (+3 oxidation state) methyltransferase (AS3MT) Met287Thr polymorphism to determine whether such variants influence As-related genotoxicity. As content in the drinking water of the population was found to range between 1 and 187 microg/l, with a mean concentration value of 16 microg/l. The total urinary As content of the exposed individuals was found to be correlated with the As content in drinking water, and subjects were classified as low (< 30 microg As/g creatinine), medium (31-60 microg As/g creatinine), and highly exposed (> 61 microg As/g creatinine). A positive association was found between the level of exposure and the genetic damage measured as percentage of DNA in tail (p < 0.001), and AS3MT Met287Thr was found to significantly influence the effect (p < 0.034) among children carrying the 287Thr variant allele. Altogether, our results evidenced that people living in As-contaminated areas are at risk and that AS3MT genetic variation may play an important role modulating such risk in northern Mexico, especially among children.