We evaluated the concentrations of brain natriuretic peptide in the plasma as a marker of systolic ventricular function before and after maximal exercise in 15 surgically palliated patients with functionally univentricular hearts, with apparently good ventricular function. Of the patients, 6 with median age of 14.6 years, and a range from 12.5 to 17.9 years, had been palliated by construction of a total cavopulmonary connection, while the other 9 patients, with a median age of 32.1 years, and a range from 15.6 to 54.2 years, had undergone the classical Fontan procedure. We used 8 healthy individuals, with a median age of 13.9 years, and a range from 12.8 to 14.2 years, as a control group for the measurements of brain natriuretic peptide. The values of the peptide were significantly higher in those with the classical Fontan procedure, both before, when the median value was 131.8 nanogram per litre, with a range from 0.5 to 296.4, and after maximal exercise, when the median value was 108.1, with a range from 0.1 to 235.9. The comparable values in those with a total cavopulmonary connection were a median of 12.8, and a range from 0.5 to 39.1 before, and a median of 9.7, with a range from 2.7 to 26.2 after maximal exercise. The median value for the control group was 13.1, with a range from 2.6 to 38.7 before exercise (p = 0.016), and a median of 24.1, with a range from 5.8 to 66.7 after maximal exercise (p = 0.03), respectively. In the control subjects, the level of the peptide increased by a median of 9.7 nanograms per litre, with a range from 1.2 to 28.0 after maximal exercise (p = 0.008). The level was unchanged after maximal exercise in those with classical Fontan procedures and total cavopulmonary connections, with a difference between levels before and after exercise of a median of 5.9 nanogram per litre, and a range from −23.7 to 31.0 (p = 0.96), and a median of −1.0 nanogram per litre, with a range from −12.0 to 3.9 (p > 0.99), respectively. We conclude that maximal exercise did not increase the level of brain natriuretic peptide level in those patients with the classical Fontan procedure, nor those with a total cavopulmonary connection, findings which may indicate that systolic ventricular dysfunction is not the major cause of the decreased working capacity observed in patients with well functioning palliated functionally univentricular hearts.