The aim of the study was to evaluate the association between the frequency of cytogenetically damaged lymphocytes, glutathione- S-transferase (GST) gene polymorphisms, and mercury concentrations in the peripheral blood of mercury industry workers as well as an non-exposed local population (control group) of Aktash village, the Republic of Altay. The venous blood samples were obtained from 184 workers and 156 controls for chromosome assay, mercury blood concentration analysis, and the GSTM1 and GSTT1 gene polymorphism assessment by a polymerase chain reaction approach. Statistical analyses were carried out using Student's t-test, one-way ANOVA, or linear multiple regression. We demonstrated a significant increase in the frequency of lymphocytes with aneuploidy and polyploidy in the workers as compared with the controls (p < 0.001). The highest levels of aneuploidal and polyploidal lymphocytes were determined in the subgroup of workers with double null GSTM1(0)/GSTT1(0) genotype (p