In the present study, we identified the factors affected central obesity prevalence in the adult Altains, Russians and Tuvans permanently residing in the Altai and the Tuva Republics. The data was collected in 2018–2020. The examination program included anthropometrical examination and the genetic testing of females and males, aged 18–35 years. Anthropometrical examination was carried out in accordance with the guidelines accepted in the Research Institute and Museum of Anthropology. Body composition was analyzed by bioelectrical impedance analyzer. The SNPs rs1800592 UCP1, rs660339 UCP2 and rs1800849 UCP3 were assessed. The prevalence analyses of underweight, overweight and general obesity in the groups of female and males were conducted. The anthropometric indices were used to estimate the prevalence of central obesity. General obesity occurred more often in the group of Altai people, whereas in the Tuva people the central obesity is more pronounced. The Altai and Tuva people are alike in the total body measurements, whereas Russians were significantly higher. All studied groups demonstrated the sexual dimorphism of the body composition and waist to hip ratio. No significant differences in waist to height ratio between males and females were identified in the studied groups. No association between genetic variants and the obesity-related traits, which reflect the body fat and its distribution, was revealed. All factors included in the model are able to predict 8 % of the variability of the central obesity-related traits. Ethnic background contributes the most to the variability of the central obesity index.