To determine the predictive value of body mass index (BMI) and waist circumference (WC) and their optimal cut-off points for metabolic syndrome (MetS), and also the incidence of MetS. This study included 888 children, aged 6-12 years, who were followed for a mean of 6.6 years. BMI, WC and their optimal cut-off points to predict MetS were investigated. The cumulative incidence of MetS was 10.7%. The adjusted ORs for age, sex and family history to predict MetS for BMI and WC z-scores were 2.6 (95% CI, 2.0-3.5) and 2.6 (95% CI, 1.9-3.5), respectively. In their correspondent models, area under the receiver operating characteristic (ROC) curve was 0.73 (95% CI, 0.68-0.79) for BMI z-scores and 0.72 (95% CI, 0.67-0.78) for WC z-scores with no statistically significant difference. The optimal cut-off values for BMI were 16.5 kg/m(2) for boys and 16.3 kg/m(2) for girls and those for WC were 57.5 cm for boys and 56.5 cm for girls. Our findings suggest that both BMI and WC have the same power to predict MetS and also children with higher BMI or WC are more susceptible to MetS. Moreover, a high incidence of MetS in children highlights the importance of interventional strategies during early childhood.