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Background We sought to characterize body composition abnormalities in young patients living with a Fontan circulation and explore potential pathophysiologic associations. Methods and Results Twenty‐eight patients with a Fontan circulation were prospectively recruited in this cross‐sectional study. Participants underwent cardiopulmonary exercise testing, dual‐energy X‐ray absorptiometry, echocardiography, and biochemical assessment. Mean age was 26±7 years. Skeletal muscle mass, estimated by appendicular lean mass index Z score, was reduced compared with reference data (−1.49±1.10, P<0.001). Percentage body fat Z score overall was within normal range (0.23±1.26, P=0.35), although 46% had elevated adiposity. Those with reduced skeletal muscle mass (appendicular lean mass index Z score of −1 or lower) had lower percent predicted oxygen pulse (55±15 versus 76±16%, P=0.002). Overall agreement between body mass index and dual‐energy X‐ray absorptiometry to assess adiposity was fair only (weighted [linear] κ coefficient: 0.53; 95% CI, 0.34–0.73) and slight in the setting of muscle mass deficiency (weighted κ coefficient: 0.32; 95% CI, 0.13–0.50). Appendicular lean mass was independently associated with absolute peak VO2 (β=70.6 mL/min, P=0.001). Appendicular lean mass index Z score was inversely associated with hemoglobin (r=−0.4, P=0.04), and the degree of muscle deficit was associated with ventricular systolic impairment. Conclusions Young patients with a Fontan circulation have a body composition characterized by reduced skeletal muscle mass, which is associated with peak exercise capacity. Increased adiposity is common despite a normal body mass index. Low skeletal muscle mass is associated with systolic dysfunction and compensatory erythrocytosis.