The influence of body size and maturation on the responses in peak oxygen uptake (VO2) to a 12-week aerobic training and nutritional intervention in obese boys (n = 30; 10-16 years) was examined using multilevel allometric regressions. Anthropometry, sexual maturity status, peak VO2, and body composition were measured pre- and postintervention. Significant decrements for body mass, body mass index z-score, and waist circumference and increments for stature, fat-free mass, and peak oxygen uptake were observed after intervention. Partitioning body size on peak VO2, the responses of the individuals to training were positive (11.8% to 12.7% for body mass; 7.6% to 8.1% for fat-free mass). Body mass and fat-free mass were found as significant explanatory variables, with an additional positive effect for chronological. The allometric coefficients (k') in the initial models were k' = 0.883 and k' = 1.058 for body mass and fat-free mass, respectively. The coefficients decreased when age was considered (k' = 0.530 for body mass; k' = 0.860 for fat-free mass). Including maturity indicator in the models was not significant, thus the influence of variability in sexual maturity status in responses to exercise-based intervention in peak VO2 may be mediated by the changes in body dimensions.