Abstract Background The aim of this review is to understand the clinical usefulness of Brain Natriuretic Peptide (BNP) and N-terminal pro-Brain Natriuretic Peptide (NT-proBNP) in pediatric cardiology. Methods A computerized literature search on National Library of Medicine using the keywords “BNP assay” and “NT-proBNP assay” was performed. Then, we refined the analysis to include only the studies specifically designed to evaluate the clinical usefulness of BNP and NT-proBNP assays in patients with congenital heart disease. Results BNP and NT-proBNP are useful marker for diagnosis of heart failure, for the assessment of clinical severity and for the follow-up of congenital and pediatric heart diseases. However, results from different studies are often partial and not always univocal. Moreover, reference intervals in pediatric population have not yet been extensively evaluated. Conclusions BNP and NT-proBNP may be considered helpful markers for the integrated diagnosis and management of pediatric patients, though further studies are needed to support their routine use.