We examined the impact of varying degrees of obesity on the prevalence of the metabolic syndrome and its relation to ectopic fat deposition in a large, multi-ethnic cohort of children and adolescents. A standard glucose tolerance test was administered to 438 obese, 31 overweight and 20 nonobese children and adolescents. Baseline measures included blood pressure and plasma lipid and insulin levels. In a subset of 118 subjects, abdominal fat distribution was measured by magnetic resonance imaging (MRI) and further stratified into tertiles based on the proportion of abdominal fat in the visceral depot. Liver fat was measured by fast MRI and intramyocellular fat by proton magnetic resonance spectroscopy. Overall, the prevalence of the metabolic syndrome increased with the severity of obesity. In the subset of 118 obese adolescents undergoing MRI, there were no differences in age or body mass index z-scores across tertiles. However, as the proportion of visceral fat increased, subcutaneous fat decreased. There were significant increases in the occurrence of hepatic steatosis, insulin resistance and metabolic syndrome, with subjects in tertile 3 being 5.2-times more likely to have the metabolic syndrome than those in tertile 1. The prevalence of the metabolic syndrome is high in obese children and adolescents and increases with worsening obesity. Obese adolescents with a high proportion of visceral fat and relatively low abdominal subcutaneous fat have a phenotype reminiscent of partial lipodystrophy: hepatic steatosis, profound insulin resistance and an increased risk of the metabolic syndrome.