Adiponectin plays a protective role against atherosclerosis. Genetic investigation has revealed that G276T adiponectin gene polymorphism is related to adiponectin concentration and metabolic disturbances. The aim of the present study was to investigate the association of adiponectin gene G276T polymorphism with indices of atherosclerosis in obese children. We examined 159 children (125 obese and 34 non-obese). G276T of adiponectin gene polymorphism was identified using a PCR-RFLP method. The intima media thickness (IMT) was evaluated in 82 patients. In all children, the anthropometric indices, fasting plasma total cholesterol (TC), HDL and LDL cholesterol, triglycerydes (TG), C-reactive protein (CRP), and adiponectin were measured. Oral glucose tolerance test (OGTT) also was performed. We found that the obese patients presented with higher values of atherogenic indicators than the non-obese patients. The indicators positively correlated with CRP and lipid concentrations. Ninety one percent of obese children presented with elevated IMT which correlated with CRP. The children with GG genotype (GG + GT allele) had lower values of BMI, TC, and TG but higher adiponectin concentrations. The mean level of adiponectin was statistically decreased in the compared with the homozygous TT children. The other anthropometric and atherogenic indicators did not differ between these two sets of obese children. We conclude that adiponectin concentrations were decreased in children with polymorphism G276T in adiponectin gene. The study, however, failed to show significant associations between carotid IMT, lipid markers, blood pressure, or HOMA-IR in obese children.