The aim of this study was to investigate, in markedly obese children, the effect of puberty on substrate oxidation during an acute bout of exercise. Two groups of markedly obese boys (7 pre pubertal, 8 post pubertal, matched for adiposity) performed an exercise-test designed for measuring carbohydrate and fat oxidation with indirect calorimetry, and consisting of five six-minute steady-state workloads at 20, 30, 40, 50, and 60 % of the theoretical maximal aerobic power. Fat oxidation (mg . min (-1)) is correlated to fat free mass (FFM) (r = 0.7, p = 0.02). When expressed in crude flow rate units, fat oxidation is slightly higher in PostP than PreP children (p < 0.05). However, when expressed per unit of FFM or as a percentage of total fuel oxidation, fat oxidation is lower in PostP than PreP children (p < 0.05). Multivariable analysis shows that the influence of age on the ability to oxidize fat at exercise is explained by the pubertal increase in FFM. In markedly obese children during puberty, the ability of each kg of FFM to oxidize fat at exercise decreases (- 28% at 20%Wmax th), but the pubertal increase in FFM overcomes this effect, resulting in an increase in whole body ability to oxidize fat at exercise (+ 17,3% at 20%Wmax th).