Congenital heart disease is the most common congenital abnormality. The long-term prognosis of these patients has changed significantly over the last half century, thanks to improvements in cardiovascular diagnosis, surgery and postoperative care. However, residual lesions are not uncommon and many of the interventions performed remain palliative rather than reparative, leading to the development of ventricular dysfunction and heart failure. Natriuretic peptides are well-established markers of disease severity and prognosis in patients with heart failure due to noncongenital (acquired) heart disease. However, the role of biomarkers in congenital heart disease is unclear. This review highlights the impact of neurohormonal activation in patients with congenital heart disease, as well as the usefulness of assessing natriuretic peptide levels in specific clinical situations.