Interest in brain natriuretic peptide (BNP) and N-terminal pro-brain natriuretic peptide (NT-proBNP) in the management of children with CHD has increased. There are, however, no current guidelines for their routine use. The aim of this review article is to provide an update on the data regarding the use of BNP/NT-proBNP in the evaluation and surgical treatment of children with CHD. BNP/NT-proBNP levels in children with CHD vary substantially according to age, laboratory assay methods, and the specific haemodynamics associated with the individual congenital heart lesion. The accuracy of BNP/NT-proBNP as supplemental markers in the integrated screening, diagnosis, management, and follow-up of CHD has been established. In particular, the use of BNP/NT-proBNP as a prognostic indicator in paediatric cardiac surgery has been widely demonstrated, as well as its role in the subsequent follow-up of surgical patients. Most of the data, however, are derived from single-centre retrospective studies using multivariable analysis; prospective, randomised clinical trials designed to evaluate the clinical utility and cost-effectiveness of routine BNP/NT-proBNP use in CHD are lacking. The results of well-designed, prospective clinical trials should assist in formulating guidelines and expert consensus recommendations for its use in patients with CHD. Finally, the use of new point-of-care testing methods that use less invasive sampling techniques – capillary blood specimens – may contribute to a more widespread use of the BNP assay, especially in neonates and infants, as well as contribute to the development of screening programmes for CHD using this biomarker.