Very few large studies in Latin America have evaluated the association between waist:height ratio (W-HtR) and cardiometabolic risk in children and adolescents. Further, multivariable analyses verifying the independence of located subcutaneous fat have not been conducted so far. The aim of this study was to evaluate the associations of W-HtR and waist circumference (WC) with metabolic syndrome abnormalities and high LDL-cholesterol levels in schooled adolescents before and after adjusting for trunk skinfolds and BMI. The sample consisted of 831 boys and 841 girls aged 10–17 years. Biochemical, blood pressure and anthropometrical variables were measured. Age- and sex-specific quartiles of W-HtR and WC were used in Poisson regression models to evaluate the associations. High WC values (highest quartile v. quartiles 1–3) were associated with high TAG levels in both sexes (prevalence ratio, boys: 2·57 (95 % CI 1·91, 3·44); girls: 1·92 (95 % CI 1·49, 2·47); P<0·05), and with high blood pressure specifically in female adolescents (3·07 (95 % CI 1·58, 5·98); P<0·05), independently of trunk skinfolds or BMI (P<0·05). Associations of high WC with high fasting glucose (boys), low HDL-cholesterol and having at least two abnormalities did not remain significant in most of the adjustments for trunk skinfolds or BMI (P>0·05). High W-HtR (highest quartile v. quartiles 1–3) was only independently associated with high TAG in female adolescents (1·99 (95 % CI 1·55, 2·56); P<0·05). In conclusion, WC showed better association with cardiometabolic risk than W-HtR in the children of this study. This observation does not support W-HtR as a relevant adiposity marker for cardiovascular and metabolic risk in adolescence.