To evaluate the effect of changes in aerobic fitness and physical activity on changes in lipoproteins, we measured body composition, peak V̇O2, vigorous and sedentary activity, maturation, and lipoproteins in 125 children (mean baseline age, 10.5 years) for 5 years. Change in variables was analyzed using the slopes of the regression line obtained by plotting the data for each child. No predictor variables were significant for girls. In boys, predictors of favorable changes in lipoproteins included decreases in fatness, increases in fitness, early maturation, and increases in fat-free body mass (FFM). Multivariable analysis, adjusted for baseline age, indicated that change in FFM explained 21% of the variability in change in LDL-C. Results suggest that during puberty, changes in activity and fitness do not predict changes in lipoproteins.