The objective of this research was to study lung function, physical capacity, and effect of endurance training in children and adolescents after Fontan palliation compared with healthy matched controls. Fontan patients (n=30) and healthy matched control patients (n=25) performed dynamic and static spirometry, and pulmonary diffusing capacity and maximal oxygen uptake tests, before and after a 12-week endurance training programme and at follow-up after 1 year. Fontan patients had a restrictive lung pattern, reduced pulmonary diffusing capacity (4.27±1.16 versus 6.61±1.88 mmol/kPa/minute, p<0.001), and a reduced maximal oxygen uptake (35.0±5.1 versus 43.7±8.4 ml/minute/kg, p<0.001) compared with controls. Patients had air trapping with a higher portion of residual volume of total lung capacity compared with controls (26±6 versus 22±5%, p<0.05). Vital capacity increased for patients, from 2.80±0.97 to 2.91±0.95 L, p<0.05, but not for controls after endurance training. The difference in diffusing capacity between patients and controls appeared to be greater with increasing age. Fontan patients have a restrictive lung pattern, reduced pulmonary diffusing capacity, and reduced maximal oxygen uptake compared with healthy controls. Endurance training may improve vital capacity in Fontan patients. The normal increase in pulmonary diffusing capacity with age and growth was reduced in Fontan patients, which is concerning. Apart from general health effects, exercise may improve lung function in young Fontan patients and should be encouraged.