It is still uncertain if cardiac natriuretic peptides are useful biomarkers in paediatric cardiology. In this review we identify four clinical scenarios in paediatric cardiology, where clinical decision-making can be difficult, and where we feel the paediatric cardiologists need additional diagnostic tools. Natriuretic peptide measurements could be that extra tool. We discuss and suggest N-terminal pro-B-type natriuretic peptide and B-type natriuretic peptide reference intervals for children without cardiovascular disease and cut-off points for the four specific paediatric heart conditions. We conclude that in premature neonates with persistent arterial ducts; in teenagers with tetralogy of Fallot and pulmonary regurgitation; and in children with heart transplants and potential allograft rejection cardiac peptides can provide the clinician with additional information, but in children with atrial septal defects the peptides are not helpful in guiding treatment or follow-up.