The purpose of this study was to examine the effect of 12 wk of aerobic exercise on lipid profiles, antioxidant enzyme activities, oxidative products, and autonomic nervous activity (ANA) in children with obesity. We studied 16 children with obesity and 19 age-matched normal weight controls over a period of 12 wk, during which time moderate intense running exercise was performed. Measurements included peak oxygen uptake, body composition, blood lipid profiles, ox-LDL, 8-OHdG, SOD, GPx activities, total mRNA, and ANA. There were no differences in body weight between periods in the OW group, but body weight increased after 12 wk in OR and CO groups. There were no differences in WHR between periods in the OR and CO groups, but the WHR values decreased after 12 weeks in the OW group. In the obese group, the baseline TG was higher than in the controls (p<0.05), while the ANA level was lower. There were differences in antioxidant enzyme gene expressions between periods in all groups. In conclusion, oxidative damage and antioxidant enzyme activities in obese children were found to be similar to those of normal weight children. However, TG was higher and ANA was lower in obese children than in normal weight children. These results indicated that increased TG and decreased ANA levels begins in childhood in obese patients. Also, regular aerobic exercise may modify the antioxidant enzyme gene expression in early life.