In some forms of congenital heart disease, such as D-transposition of the great arteries, and when there is only a single ventricle such as with hypoplastic left heart syndrome, a hole between the upper chambers of the heart (the atria) is necessary to allow adequate mixing of oxygen-rich blood returning from the lungs to the heart and then to the body. This generally must be performed shortly after birth.

The most common method is called a Rashkind atrial septostomy. This was the first interventional catheter-based procedure performed on infants born with heart disease (D-transposition of the great arteries). A special balloon-tipped catheter is introduced from the femoral vein or the umbilical cord vein and advanced across the small natural hole between the atria (patent foramen ovale, or PFO). The balloon is inflated in the left atrium and forcibly drawn back to create a tear, which enlarges the PFO and allows blood to pass more easily across the atria. This procedure can be performed in the cardiac catheterization lab or at the bedside in the intensive care unit.

For some patients, this hole must be present for several months before more definitive surgery. Occasionally, the hole that was created can become smaller and require a repeat catheter-based septostomy. Sometimes another Rashkind balloon catheter can be used, but sometimes the atrial septum becomes thicker over time and cannot be easily opened with the Rashkind catheter. Two alternate approaches include using several larger balloons to stretch the hole (static balloon septostomy) or placing a metal stent to keep the hole from constricting again.

In some patients, no natural hole exists between the atria (intact atrial septum). If the baby has hypoplastic left heart syndrome or other single-ventricle defects where blood returning from the lungs to the left atrium has nowhere to go easily, this creates a very dangerous situation after birth. An emergency catheterization procedure may need to be performed to create a hole in the atrial septum. This hole can be initially created using a long needle that is introduced from a vein in the groin (transseptal puncture) or by using a special wire and catheter that uses radiofrequency energy to burn a hole through the septum. Following the creation of the initial hole, further enlargement can occur using progressively larger angioplasty balloons or by placing a metal stent across the atrial septum.