Recently independent studies, including genome-wide scans, have shown that the rs9939609 single-nucleotide polymorphism (SNP) in the first intron of the fat mass and obesity associated (FTO) gene were significantly associated with obesity in populations of European origin, in certain Asian (e.g.,Japanese and Chinese) and African American populations. In this study we examined the association between rs9939609 FTO variant and obesity related parameters in 394 individuals (262 males and 132 females; ages 20-70 years) from the Sverdlovsk area, Russia. A SNP variant rs9939609 was genotyped with the use of an allelic discrimination assay. The TaqMan-based real-time PCR method was applied. The prevalence of TT, TA and AA genotypes of rs9939609 FTO gene of this study was 34%, 47.5%, 18.5%, respectively, the minor A-allele frequency was 42.3%. In comparison to males, females had significantly higher the frequency of minor A-allele and AA genotype. The AA genotype was significantly more frequent in obese individuals (defined as body mass index > or = 30 kg/m2) than in non-obese (27.7 and 13.0%, respectively). Compared to the carriers of TT genotype, the likelihood of obesity was 3.0 for the carriers of AA genotype and 1.73 for the carriers of AA+AT genotype. These results confirm that genetic variation (rs9939609) FTO gene contributes to the etiology of obesity in the Sverdlovsk area.