There is no consensus on whether or not the diagnostic criteria of metabolic syndrome (MS) defined for adults [National Cholesterol Education Panel (NCEP) and World Health Organization (WHO)] can be used in childhood as well. We aimed to compare prevalence of metabolic syndrome among obese children and adolescents using WHO and NCEP guidelines. A total of 112 obese children and adolescents were assessed. MS was diagnosed according to both modified WHO and NCEP criteria using cut-off values for children. Abnormal glucose homeostasis was identified in 46.6% of the subjects. Fasting glucose levels for all subjects were less than 110 mg/dl and no subjects had type 2 diabetes. Overall, dyslipidemia was present in 42.9% and hypertension in 42.9% of the subjects. While 24% of the subjects were diagnosed as MS according to NCEP, a rate of 38.8% were diagnosed according to WHO-defined MS. There was a moderate agreement between NCEP and WHO guidelines. More children were diagnosed as MS based on the WHO guidelines. This may lead to better monitoring for these children and prevention of their chronic diseases in the future. Therefore, we recommend using WHO guidelines in the diagnosis of MS with a specific emphasis on definition of abnormal glucose homeostasis.