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The purpose of this study was to compare longitudinal trajectories of maximal aerobic capacity in children with sickle cell anemia (SCA) and matched healthy controls, and explore whether these trajectories were associated with selected physiologic variables.Children with SCA (n = 33) and healthy controls (n = 30) matched at baseline for race, sex, Tanner stage, height, and weight completed three consecutive annual fitness assessments (VO2peak). Data were compared between the groups at each time point and within groups over time. Change in VO2peak between the two groups over time was assessed using a linear mixed model with age, sex, fat-free mass (FFM), Tanner stage, and hemoglobin (Hgb) concentration as covariates.At baseline, children with SCA had significantly lower Hgb concentration (8.9 vs. 13.7 g/dL, P < 0.001) and relative VO2peak (24.2 vs. 27.9 ml/kg/min, P = 0.006) than healthy controls. Over time, children with SCA had smaller increases than healthy controls in VO2peak (−0.1 and +4.9 ml/kg/min, P < 0.001), Tanner stage at year 2 (15% and 66% Tanner 4, P < 0.001), and FFM (+4.0 and +6.8 kg, P = 0.02). Changes in Hgb concentration did not differ between groups (+0.03 and +0.09 g/dL, P = 1.0). After adjusting for age, sex, Tanner stage, FFM, and Hgb concentration the differences in change in VO2peak over time remained significant (P < 0.001).Children with SCA demonstrate lower relative VO2peak compared to healthy children and the difference increases over time. The difference in VO2peak trajectories between the two groups during puberty remains significant after adjusting for age, sex, FFM, Tanner stage, and Hgb concentration. Pediatr Blood Cancer 2015;62:648–653. © 2014 Wiley Periodicals, Inc.