Objective To compare the effectiveness of three waist circumference (WC) measurement sites to predict cardiovascular risk factors and metabolic syndrome (MS) in Brazilian children. Methods 187 children (mean age = 9.9 ᠰ.7 years) were evaluated for weight, height, WC at three different sites: midpoint between the lower rib and iliac crest (WC1), umbilicus (WC2), and narrowest waist (WC3). Skinfolds (triceps and subscapular) and blood pressure were also measured. Analyses for triglycerides, HDL-C and glucose were carried out in 141 children. Results For boys, the most accurate predictor of overweight and obesity (from body mass index, BMI) and low HDL-C levels was WC3, and for high percentage of body fat (from skinfolds) was WC1. For girls, WC2 was the most accurate predictor of MS, and hypertriglyceridemia, and for overweight and obesity, high body fat percentage, and low HDL-C levels, WC3 was the best predictor. WC1 was the most accurate in the prediction of high blood pressure. Conclusions Each WC measurement site was accurate in predicting cardiovascular risk factors and MS. However, our results indicate that WC3 was the best predictor of cardiovascular risk factors and MS in boys and girls.