This study examined the relationships between serum adiponectin (AD) and leptin (LP) levels, and obesity using a population-based cohort consisted of 315 (9–10 year olds: G1) and 308 (12–13 year olds: G2) school children. Serum AD, LP and other markers were compared according to the presence of obesity.The prevalence rates of obesity were 14.9% in G1 and 9.4% in G2. The medians of serum AD (μg/dl: non-obese/obese) were statistically lower in obese children (9.6/8.3 in G1, p<0.05; 8.9/6.6 in G2, p<0.05), and the medians of serum LP (ng/dl) were statistically higher in obese children (3.7/12.5 in G1, p<0.05; 2.9/8.4 in G2, p<0.05). The serum LP levels were significantly positively correlated with percent overweight (POW) irrespective of age and sex, and the serum AD levels were significantly negatively correlated with POW except for boys in G1. Multivariate regression analyses revealed that LP, LDL-cholesterol and gender in G1, and LP, AD, blood pressure and gender in G2 were significantly correlated with POW.A large-scale, population-based study revealed that AD was lower and LP higher in obese children, and that the obese status in G2 was related to a worse metabolic profile than the case in G1.