The aim of this study was to generate normal values of amino-terminal pro-brain natriuretic peptide (NT-pro-BNP) in children and adolescents after Fontan operation without congestive heart failure (CHF) and to test the hypothesis that plasma levels of NT-pro-BNP correlate with the clinical severity of CHF. NT-pro-BNP plasma levels of 59 consecutive patients, with a median age of 8.4 years, after Fontan operation were measured using an automated enzyme immunoassay. The 97.5th percentile of NT-pro-BNP in patients without CHF was 282.3 pg/ml. The severity of heart failure was quantified by a pediatric cardiologist using the New York University Pediatric Heart Failure Index (NYUPHFI). NT-pro-BNP levels correlated with the NYUPHFI (p = 0.001). In patients with CHF (14/59) the NT-pro-BNP levels were significantly higher (median, 399 pg/ml; range, 140-5440 pg/ml) than in patients without CHF (median, 96 pg/ml; range, 11-376 pg/ml). NT-pro-BNP levels of patients with Fontan circulation without CHF are similar to those of healthy children. Plasma NT-pro-BNP concentrations correlate with the severity of CHF in children and adolescents after Fontan operation. Plasma NT-pro-BNP levels can help clinicians in the detection of CHF in pediatric patients with Fontan circulation.