Objective: The study aimed to determine the incidence of metabolic syndrome (MS) in a group of Czech obese children, to evaluate the incidence of insulin resistance according to HOMA-IR in this group, and to consider the diagnostic value of HOMA-IR in early MS detection in obese children using the logistic regression models for analyzing the relations between HOMA IR and MS. Subjects and Methods: Anthropometric and laboratory examinations were performed in a group of 274 obese children aged 10-17 years. Results: MS was established in 102 subjects (37%). The presence of insulin resistance according to HOMA-IR >3.16 was ascertained in 53% of the subjects. HOMA-IR limit was exceeded by 70% in the MS (+) group and by 43% in children in the MS (-) (p<0.0001) category. Conclusion: The relatively high incidence of insulin resistance in obese children without MS questions the prevailing diagnostic criteria of, perhaps, falsely excluding some cases of, MS.