In this study, we aimed to estimate the association between the rs9939609 FTO (fat mass and obesity associated) polymorphism and a risk of overweight in children living in the Baikal region. We performed a case - control study that included 113 schoolchildren living in industrial centers of the Baikal region (Irkutsk, Angarsk, and Ulan-Ude). Anthropometric parameters were measured and body mass index was calculated with its values being ranked in accordance with the WHO BMI curves depending on a sex and age. Genotyping of the rs9939609 FTO polymorphism was performed by allele-specific amplification with real-time results detection. To assess likelihood of an association between the FTO gene allele and overweight and obesity, relative risk (RR) and 95 % confidence interval (CI) were calculated.The assessment revealed the A allele of the rs9939609 FTO polymorphism to be by 1.29 times more frequent in the examined children with overweight and obesity (48.44 %) than in the children from the reference group (37.65 %). The FTO rs9939609 polymorphism was authentically associated with likelihood of elevated risks of overweight and obesity in children with the homozygous AA genotype (RR = 2.806, 95 % CI: 1.650-4.772; STD = 0.271). Our study confirms that the rs9939609 polymorphism of the FTO gene is a risk factor of overweight and obesity for children from the Baikal region who have the A allele of the homozygous AA genotype. Prevailing frequency of the TT genotype (29.2 %) as compared with the AA genotype (10.62) is likely due to influence of assimilation processes on urbanized territories in the Baikal region.