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The clinical usefulness of B-type natriuretic peptide (BNP) assay in congenital heart diseases is still controversial. We evaluated the diagnostic accuracy and clinical relevance of this assay in different cardiovascular hemodynamic conditions in pediatric patients with congenital heart diseases.BNP was measured in 173 healthy individuals and in 382 pediatric patients with congenital heart diseases. We identified five subgroups of hemodynamic conditions: left ventricular volume overload, right ventricular volume overload, left ventricular pressure overload, right ventricular pressure overload, and biventricular volume overload.BNP was higher (P < 0.0001) in patients (median 49.0 ng/l, range 0.45–14363 ng/l) than in the reference population (median 6.1 ng/l, range 1.0–29.7 ng/l). BNP assay showed a good diagnostic accuracy in discriminating between healthy individuals and patients (area under the receiver operating characteristic curve 0.95, SE 0.009). Lower BNP values were found in right ventricular pressure overload than in left ventricular pressure overload, left ventricular volume overload, or biventricular volume overload. In the left ventricular volume overload subgroup, BNP significantly correlated with peak systolic gradients (ρ = 0.622, P < 0.001) and left ventricular dilatation (ρ = 0.35, P = 0.03). In the right ventricular volume overload subgroup, BNP correlated with right ventricular pressure (ρ = 0.622, P < 0.001) and right ventricular dilatation (ρ = 0.377, P = 0.0077). Moreover, in cyanotic defects, BNP showed a significant correlation with O2 saturation (ρ = 0.204 P = 0.0128).BNP assay showed a good diagnostic accuracy in discriminating between healthy individuals and patients. Congenital heart disease with left ventricular pressure overload and biventricular volume overload has higher BNP values than that with right ventricular pressure overload.