Childhood and adolescent obesity is highly prevalent and a relevant public health problem in Chile. Metabolic syndrome (MS), which is predictive of future cardiovascular disease and type 2 diabetes, has been associated with childhood obesity and insulin resistance. The aim of this study was to determine the prevalence of MS in a non-consultant obese adolescent population and to assess the underlying factors for the MS in these subjects. The nutritional status was evaluated for 25,102 students from 10 to 18 years of age living in Concepcin and Coronel, Chile. A total of 2,308 adolescents were found to be obese (BMI > or = 95 percentile). Metabolic syndrome was defined as the presence of at least three of the following abnormalities: waist circumference > or = 90th percentile, blood pressure > or= 90th percentile, fasting glycaemia > or = 100 mg/dL, HDL-cholesterol < or = 40 mg/dL and triglycerides > or = 110 mg/dL in a representative sample of 461 adolescents. The results obtained indicate that the prevalence of obesity was 9.2% and that MS reached 37.5%. Only 4.1% of the adolescents failed to present any of the risk factors for MS. When compared with the adolescents without MS, the estimated odd ratios (OR) for the presence of the characteristics of MS were all statistically significant, with increased waist circumference reaching an OR of 21.56. A significant difference was found between adolescents with and without MS; the parameters indicated greater insulin resistance for adolescents with MS. In conclusion, MS is highly prevalent among Chilean adolescents with obesity and its prevention beginning in childhood needs to be addressed.