AIM: To compare the expression levels of the adiponectin and peroxisome proliferator -activated receptor gamma (PPARgamma) genes in subcutaneous adipose tissue (SC) and omental adipose tissue (OM) in children with relation to age and anthropometric variables. METHODS: Paired biopsies (SC and OM) were obtained from 53 children (age 0.2-14 years, BMI 12.5-25.8 kg/m(2)). Adiponectin and PPARgamma mRNA levels in adipose tissue were measured by real-time PCR. RESULTS: In overweight, but not in normal weight children, the median adiponectin mRNA level was significantly lower in OM [0.51 (0.1-2.17)] compared to SC [1.29 (0.16-5.08)], (p = 0.03). Adiponectin mRNA levels were strongly associated with PPARgamma mRNA levels in both SC (r = 0.73, p < 0.001) and OM (r = 0.78, p < 0.001). CONCLUSIONS: The lower adiponectin expression in OM relative to SC in overweight children indicates that metabolic-endocrine alterations begin already in childhood. The close association between adiponectin and PPARgamma expression supports the hypothesis this transcription factor is involved in adiponectin gene regulation.