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Objectives: B-type natriuretic peptides have been shown to enable differentiation between heart and lung diseases in adults and children. In neonates, the role of natriuretic peptides for diagnosis of congenital heart defect (CHD) is not yet ascertained. The purpose of this single-center prospective study was to investigate aminoterminal B-type natriuretic peptide concentrations and their time courses during the first 5 days of life in neonates with CHD compared with neonates with respiratory distress., Design: Single-center prospective study., Setting: Tertiary-care neonatal ICU., Patients: Aminoterminal B-type natriuretic peptide levels of 40 neonates with arterial duct-dependent CHD and of 40 neonates with respiratory distress without CHD were analyzed on the first, second, third, and fifth day of life., Main Results: Mean aminoterminal B-type natriuretic peptide concentrations in the CHD group were significantly higher on the second (14191 vs. 4872 pg/mL), third (17790 vs. 3524 pg/mL), and fifth day (17015 vs. 4044 pg/mL), but not on the first day of life. Repeated measurements analysis of variance revealed a significantly different time course of aminoterminal B-type natriuretic peptide concentrations between the two groups., Conclusions: On the first day of life, aminoterminal B-type natriuretic peptide cannot differentiate between CHD and respiratory distress without CHD in the neonate. From the second day onwards, aminoterminal B-type natriuretic peptide in neonates with CHD shows higher values and a different time course and enables differentiation between CHD and respiratory distress due to other than cardiac reasons.