Introduction: In the light of recent studies, the usefulness of the metabolic syndrome diagnosis in obese pediatric patients seems to be controversial. It leads to the pressing questions, if the metabolic syndrome diagnosis is reflecting risk of the cardiovascular complications in obese children. Aim of the study: To evaluate the incidence of metabolic syndrome in obese children, asses the role of insulin resistance in the metabolic complications and investigate if the diagnosis of MS has a clinical value in that group of patients. Material and methods: After the retrospective analysis of 588 records of obese children treated in metabolic outpatient clinic, 289 children (145 boys) in the mean age of 11 years, was qualified to the study. Diagnosis of metabolic syndrome was based on IDF 2009 criteria and HOMA-IR was used in the assessment of insulin resistance. Results: Metabolic syndrome was diagnosed in 69 children (24%) including 42 girls (61%, p < 0.05). Mean age was higher (12.4 vs. 10.9, p < 0.05) in patients with metabolic syndrome. Initial BMI Z-score was similar in the both groups (2.93 SD vs. 2.92 SD). However, further follow-up showed significantly (p < 0.001) less effective BMI z-score reduction in patients with metabolic syndrome. Insulin resistance was observed significantly more often in children with metabolic syndrome (77% vs. 35%, p < 0.0001). Moreover, aminotransferases were significantly higher in boys with metabolic syndrome (AST = 35 vs. 28 U/l, ALT = 38 vs. 23 U/l, p < 0.0001). Conclusions: The diagnosis of metabolic syndrome in obese children seems to have a predictive value for the clinical practice. Affected children are older and their criteria are present more often in girls. Insulin resistance seems to be an important factor associated with metabolic syndrome in obese children. The outcomes of behavioral therapy are less effective in children with metabolic syndrome. Affected boys are at higher risk of non-alcoholic fatty liver disease (NAFLD) in the future.