Background: The adiponectin gene has been identified as a susceptibility locus for metabolic syndrome, diabetes and cardiovascular disease. Aim: To examine the influence of two single nucleotide polymorphisms (SNPs) of this gene (+276G>T and +45T>G) on circulating adiponectin concentrations, and to evaluate their relationship with adiposity and cardiometabolic risk factors in prepubertal children with and without abdominal obesity. Material and methods: 168 children (78M, 6-10 years) were examined, divided into three groups based on waist circumference (WC). Auxological and biochemical parameters were measured by standard procedures. Adiponectin SNPs were genotyped using TaqMan allelic discrimination assays. Results: Adiponectin concentration correlated inversely with measures of adiposity (rBMIzscore=- 0.211, pBMIz-score=0.007; rwc=-0.210, pwc=0.008; rwc/height=-0.215, pwc/height=0.006), and was significantly influenced by blood glucose, insulin and systolic blood pressure (SBP). The +276T-allele carriers had higher SBP and diastolic BP compared to GG-homozygotes (p<0.05), and expressed higher obesity-related measures and lower adiponectin concentrations. As to the +45T>G SNP, the GG-subject had higher total cholesterol and LDLC concentrations compared to the T-allele carriers (p<0.05), showing worse obesity measures, higher triglyceride, glucose and insulin and lower serum adiponectin values. Conclusion: Genetic variants of the adiponectin gene had an impact on adiposity, adiponectin concentrations and some cardiometabolic variables among prepubertal children.