The purpose of this study was to investigate the outcome in infants with hypoplastic left heart syndrome and intact atrial septum and to evaluate the relationship of atrial morphology, left atrial decompression pathway and lung histopathology to outcome. In the hypoplastic left heart syndrome, severe restriction at the atrial level results in marked systemic hypoxemia after birth. Infants with intact atrial septum may be at high risk for mortality after Norwood operation. Of 316 infants with hypoplastic left heart syndrome seen at our center over a 6.5-year period, 18 (5.7%) had intact atrial septum. Medical records and echocardiograms were reviewed. On echocardiography, three types of intact atrial septal morphology were identified: 1) large left atrium, thick prominent septum secondary with thin septum primary adherent (type A, n = 12); 2) small left atrium with thick, muscular atrial septum (type B, n = 4), and 3) giant left atrium, thin atrial septum with severe mitral regurgitation (type C, n = 2). Seven infants had left atrial decompression pathways that were severely obstructed (3/12 type A, 4/4 type B). Norwood operation was performed in 17 infants; one underwent emergency balloon atrial septostomy and died. Of six early survivors, all with type A atrial morphology and unobstructed decompression pathway, three died after subsequent cavopulmonary surgery. Lung histopathology revealed severely dilated lymphatics and "arterialization" of the pulmonary veins in those with the severest degree of obstruction to left atrial egress (type B atrial morphology). Despite aggressive intervention, outcome for infants born with hypoplastic left heart syndrome and intact atrial septum is poor. Maldevelopment of the pulmonary vasculature contributes to the high mortality seen. Atrial morphology can be used as a marker for the severity of pulmonary vascular disease.