The purpose of the present study was to investigate the thermic effect of food (TEF) and sympathetic nervous system (SNS) activity in obese boys. Ten obese (9.2 ± 0.4 years) and 13 lean boys (8.8 ± 0.4 years) were examined for energy expenditure and fat oxidation measured via indirect calorimetry for 3 hours after a high-carbohydrate (HC; 70% carbohydrate, 20% fat, and 10% protein) or a high-fat (HF; 20% carbohydrate, 70% fat, and 10% protein) meal served on 2 different days at random. The activity of the SNS was assessed by means of a power spectral analysis of the heart rate variability. The TEF, expressed as a percentage of the consumed energy, was significantly lower in obese boys than in lean boys after the HC meal; however, such a difference was not observed after the HF meal. Multiple regression analysis revealed that obesity was a significant variable contributing to the variances in the TEF induced by the HC meal. Moreover, after the HC meal, the boys with a recent onset of obesity (duration, <3 years) manifested a lower TEF as well as a reduced very low frequency component of the heart rate variability, an index of thermoregulatory SNS functions, compared with the remaining obese and lean boys. In conclusion, obese boys possessed normal metabolic and sympathetic responses to the HF meal but showed a diminished thermogenic response to the HC meal, especially during the early phase of obesity.