Atrial septal ablation is performed in the treatment of congenital heart disease by inserting an instrument through a blood vessel in the patient's thigh, bringing the instrument to the heart to block holes in the heart or widen narrow areas in the heart. heart valves or blood vessels.

Many congenital heart diseases, especially severe congenital heart disease in the neonatal period, require emergency atrial septal surgery in order to better mix blood in the atrium and reduce right atrial pressure.