While increased plasma brain natriuretic peptide (BNP) levels have been documented late after the Fontan procedure, its significance remains unclear. We sought to test the hypothesis that plasma BNP levels reflect systemic ventricular function after the Fontan procedure by interrogating the relationship between plasma BNP level and indices of ventricular function. The plasma BNP levels and systemic ventricular function, as determined by conventional and tissue Doppler assessments, acoustic quantification (AQ), and myocardial performance index (MPI), of 35 asymptomatic Fontan patients were compared to those of 34 control subjects who had previous repair of ventricular septal defect. When compared with controls, Fontan patients had significantly higher plasma BNP levels (median 21 pg/ml, range 5-397 vs median 15 pg/ml, range 5-62, P = 0.04). Their systolic and diastolic ventricular function was impaired as evidenced by reduced systemic ventricular early diastolic (E) inflow velocity, early to late (A) diastolic inflow velocity ratio, left and right annular early diastolic (e), late diastolic (a), and systolic (s) velocities, AQ-derived ventricular fractional area change, peak emptying rate, and peak filling rate, and increased AQ-derived atrial filling fraction and MPI (all P < 0.05). Plasma BNP levels correlated negatively with E and A velocities, left-sided annular a velocity, and right-sided annular e, a, and s velocities, and positively with AQ-derived atrial filling fraction (all P < 0.05). In conclusion, our findings suggest that plasma BNP levels reflect primarily the diastolic function of the systemic ventricle in asymptomatic Fontan patients.