Interleukin-6 (IL-6) is a pleiotropic cytokine expressed in many tissues. A polymorphism in the IL-6 gene, associated with differences in IL-6 transcription rate, has been recently described. Subjects with the -174GG genotype are prone to lipid abnormalities. We investigated the effect of the G-174C IL-6 polymorphism on health indices and lipid values of 184 Greek primary school children. The genotype distribution of the polymorphism was 37.5% for GG and 52.2% and 10.3% for GC and CC, respectively. No differences were observed between genotype distribution and gender (p = 0.37). Boys homozygous for the G allele showed higher triglyceride levels than boys carrying the C allele (86 +/- 28 vs. 74 +/- 20 mg/dL, p = 0.02) and lower mid-upper arm muscle circumference (17.46 +/- 1.86 vs. 18.91 +/- 2.53 cm, p = 0.013). In addition, girls homozygous for the G allele had higher values for suprailiac skinfolds compared with those bearing the C allele (21.28 +/- 12.56 vs. 17.09 +/- 13.36 mm, p = 0.06). These findings were confirmed by multiple linear regression analysis, after controlling for age, sex, BMI, energy and total fat intake, and weekly physical activity. From the results of the present study, we concluded that individuals homozygous for G allele on the IL-6 gene have higher values in some parameters associated with obesity.