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Regional fat distribution is an important determinant of cardiometabolic risk in both adult and children and adolescents. The aim of this study was to investigate the association between the indices of fat distribution derived by Dual-energy X-ray Absorptionmetry (DXA) with cardiometabolic risk factors in obese and nonobese children and adolescents.A total of 1983 children and adolescents aged 6–18 years underwent a comprehensive assessment of cardiometabolic risk factors. Body composition was measured by Dual-energy X-ray Absorptiometry (DXA).After adjusting for age and height, almost indices of fat distribution derived by DXA presented positive relationship with the examined cardimetabolic risk factors, but displayed the negative associations with HDL cholesterol. Moreover, these significant correlations differed with age and sex. VFM was an independent predictor of TG among children aged 6–9 years (P < 0.001), and HDL cholesterol for adolescent boys (P = 0.001). AFM/GFM ratio was an independent predictor of HDL cholesterol and TG for adolescent girls (both P < 0.001). TrFM was the most important determinant of MS in boys (OR = 8.46, 95%CI:3.52–20.32, P < 0.001). For girls, VFM was the most important determinant of MS (OR = 1.01, 95%CI:1.00–1.02, P = 0.017).Among children and adolescents, almost indices of fat distribution derived by DXA presented positive versus negative associations with the examined cardimetabolic risk factors, but with significant differences seen by age and sex. The indices of fat distribution may serve as clinically useful tools for evaluating cardiometabolic risk in children and adolescents, but dependent of age and sex.