Background Metabolic syndrome (MetS) is not only a problem of adulthood but is already present in children and adolescents. The aim of this study was to estimate the prevalence of MetS in adolescents and to identify the associated factors. Methods This was a cross-sectional study with 354 overweight and obese school-aged adolescents (10-19 years). Sociodemographic, anthropometric, clinical, biochemical and lifestyle variables were collected. MetS was identified according to the criteria proposed by the International Diabetes Federation (IDF). Multivariate logistic regression models were used to examine the associations between risk variables and MetS. Results The prevalence of MetS was 9.6%. Among adolescents with MetS, all of them had low high-density lipoprotein cholesterol (HDL-c), while 76.5% had hyperglycemia and 38.2% had hypertriglyceridemia. Only 12.1% did not present any component of MetS, while 40% had at least two components. Multivariate analysis showed that being a girl was a protective factor (odds ratio [OR] = 0.29, confidence interval [CI] = 0.13-0.65) for the presence of MetS, while obesity (OR = 3.63, CI = 1.62-8.17) and being insufficiently active (OR = 4.60, CI = 1.01-20.96) were the risk factors for MetS. Conclusions Obese and insufficiently active male adolescents are more likely to have MetS. Early identification of MetS components, especially among obese adolescents, is an important tool for the prevention of cardiovascular complications in adult life.