e purpose of this study is to investigate the effects of exercise on body composition, blood lipids, BDNF, FGF and IGF-1in obese adolescents. The subjects of this study were 16 boys, who were divided into combined exercise group (EG, n = 8) and control group (CG, n = 8). The exercise program was conducted for 50-60 minutes per day, four times a week, for a 12-week period. We measured body composition (Weight, body fat mass, body fat percentage and lean body mass), lipid (TC, TG, Glucose, HDL-C,LDL-C), BDNF, FGF and IGF-1. The comparisons of mean differences before and after the intervention between group, weight (p < .05), BMI (p < .05), Glucose (p < .05) of EG decreased more significantly than CG. And the BDNF (p < .05) was more significant increased than CG. FGF and IGF-1 of EG increased more than CG. The change in BDNF after 12 weeks of exercise program had a reverse correlation with TG (r = -.770, p < .001) and Glucose (r = -.537, p < .05). The IGF-1 change at 12 weeks of exercise program is found to have a reverse correlation with percentage of body fat (r = -.525, p < .05), TC (r = -.520, p < .05), and Glucose (r = -.612, p < .05). It was found that increased BDNF after exercising influences the decrease in TG and Glucose. It is probably because increased BDNF after exercising oxidizes the glucose and TG to increase body temperature and oxygen and energy consumption. These data indicate that 12 weeks of exercise program decreased BMI and increased concentrations of BDNF in the serum.