We had two cases of neonates with hypoplastic left heart syndrome and intact atrial septum who had unique levoatriocardinal veins. Contrast-enhanced CT and angiography revealed that previously unknown communicating vessels ran from the top of the left atrium and drained into the right atrium. We emphasise that transcatheter atrial septostomy should be performed not through these communicating vessels but using the trans-septal approach in neonates with hypoplastic left heart syndrome and an intact atrial septum.