The article presents the results of a study of chromosomal mutations in residents living in the Aral Sea disaster zone. The present study was designed to evaluate the impact of the combined effect of a chemical mutagen (nickel) and bacterial microflora on the level of chromosomal aberrations (CA) in peripheral blood lymphocytes. This study used classical methods of cell cultivation, methods for determining chromosomal aberrations, a cytomorphological method for assessing epithelial cells, and an atomic absorption method for determining trace elements in the blood. The article shows that with an increase of chemical agent in the blood, the number of cells with features of damage and cells with contamination by microflora increases. Both of these factors cause an increase in the frequency of chromosomal aberrations. The article demonstrates how being exposed to a chemical factor increases chromosomal mutations, and also damages membrane components, which leads to a decrease in the barrier and protective function of the cell, and as a result also affects the level of chromosomal aberrations.