The aim of this study was to investigate the effect of short-term energy restriction combined with physical activity on changes in substrate oxidation and changes in plasma concentrations of ghrelin. We designed a longitudinal intervention study of 4.2 MJ (= 1,000 kcal) daily with exercise. Eighteen obese children and adolescents (age: 13.1 ± 1.6 years, 13 girls, 5 boys, 17 White, 1 Black) participated. We measured body mass index (BMI), plasma ghrelin, resting energy expenditure (REE), VCO2, V0 2 and respiratory quotient (RQ) at baseline and after 10 days. There was a significant decrease of BMI during the 10 day program (28.6 ± 4.3 vs 27.5 ± 4.2; ρ <0.001). Ghrelin and RQ showed a tendency to increase, but the difference did not reach significance (ghrelin: 83.4 ± 37.1 vs 99.5 ± 41.2, ρ = 0067; RQ: 0.83 ± 0.06 vs 0.85 ± 0.08, ρ = 0.433). The changes in RQ were significantly and independently correlated with the changes in plasma ghrelin (p = 0.029). The increase in RQ suggests a shift from fat oxidation towards carbohydrate oxidation. Ghrelin reflects the same sensitivity as RQ to changes in energy balance. Therefore, ghrelin seems to be a sensitive indicator for changes in substrate oxidation.