This study aims to assess the effects of a 16-week multidisciplinary program of obesity treatment on the control of metabolic syndrome (MS) and dyslipidemia in obese adolescents. Eighty-six adolescents aged 10-18 years were allocated in either the intervention group (IG; n = 44) or control group (CG; n = 42). IG was submitted to a multidisciplinary intervention based on cognitive behavioral therapy that aimed to modify eating habits and exercise behavior. We analyzed, before and after the intervention period, anthropometric parameters, body composition, bone mineral density, cardiorespiratory fitness, blood pressure, glucose, insulin, and lipid profile of the subjects. MS was classified according to International Diabetes Federation (2007) and the presence of dyslipidemia according to Back et al. (Arq Bras Cardiol 85:4-36, 2005). In the beginning of the intervention, the median number (range) of risk factors for MS present was 2.0 (0.0-5.0) in the IG and 2.0 (0.0-4.0) in the CG. After the intervention, this parameter reduced significantly in the IG (1.0 (0.0-5.0); p = 0.004) while no change was observed in the CG (2.0 (0.0-4.0); p = 0.349). In addition, we observed improvements in body mass index, waist circumference, hip circumference, maximal oxygen uptake, absolute and relative body fat, systolic blood pressure, diastolic blood pressure, and total cholesterol in the IG which was not identified in the CG. Conclusio n: We suggest that a 16-week multidisciplinary intervention based on cognitive behavioral therapy was adequate to reduce risk factors for MS in obese adolescents.