We investigated whether genetic polymorphisms in the endothelial nitric oxide (eNOS) gene (T(786)C in the promoter region, Glu298Asp in exon 7, and 4b/4a in intron 4) or eNOS haplotypes are associated with metabolic syndrome (MetS) in obese children and adolescents. We studied 242 subjects: 108 healthy (controls), 64 normotensive obese, and 70 obese children and adolescents with MetS. Genotypes were determined by Taqman(®) allele discrimination assay and real-time polymerase chain reaction (PCR), and PCR followed by fragment separation by electrophoresis. We compared the distribution of eNOS genotypes, alleles, and haplotypes in the three groups of subjects. The CC genotype for the T(786)C polymorphism was more common in the MetS group than in the control group (OR = 3.27; CI 1.81-9.07; P < 0.05). However, we found no significant differences in the distribution of eNOS haplotypes (P > 0.00625; P for significance after correction for multiple comparisons). Our findings suggest that while eNOS haplotypes are not relevant, the CC genotype for the T(786)C polymorphism is associated with MetS in obese children and adolescents. Further studies examining interactions of eNOS haplotypes with environmental factors and other genetic markers are warranted.