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Background: Previous studies have shown that older Fontan patients and those with an underlying morphologically right ventricle have lower exercise capacity. We sought to assess the natural history of exercise capacity after the Fontan operation in individual patients, and to identify the factors influencing the rate of decrease of exercise capacity over time. Methods: We studied, longitudinally, 53 Fontan patients with cardiopulmonary exercise tests (average 3.2 ± 1.1 tests for each patient). Age at the first test was 14 ± 6 years. Time intervals between tests ranged from 1 to 16 years (average, 7.7 ± 4.0 years). The morphology of the functionally single ventricle was left in 29 patients (55%) and right in 24 patients (45%). Twenty-two patients had undergone a total cavopulmonary connection (TCPC) at a mean age of 5.9 ± 2.8 years. Thirty-one patients had undergone an atriopulmonary or an atrioventricular connection at an age of 6.9 ± 4.4 years. Exercise capacity was expressed as percentage of predicted peak oxygen uptake (Vo 2). Results: Overall, peak Vo 2 decreased at a rate of −2.6 ± 2.7%/year. Ventricular morphology (r = 0.525, p = 0.0001) and type of Fontan operation (r = 0.381, p = 0.0057) appeared as the only predictors of the rate of decrease of peak Vo 2 at multivariate analysis. Patients with an underlying left ventricular morphology (−1.7 ± 2.0 vs −3.7 ± 3.2%/year, p = 0.005), and those who underwent a TCPC (−1.9 ± 1.8 vs −3.3 ± 3.2%/year, p = 0.042), had the lowest rate of decrease in peak Vo 2. Conclusions: Exercise capacity progressively declines in Fontan subjects. The decline of exercise capacity seems to be slower in patients with an underlying left ventricular morphology and in those who received a TCPC. [Copyright &y& Elsevier]