Objective: To compare the course of hypoplastic left heart syndrome (HLHS) patients diagnosed prenatally with any degree of atrial restriction with those without evidence of atrial restriction. Design: Retrospective, cohort. Methods: Prenatally diagnosed HLHS patients from August 1999 to January 2009 were categorized as nonrestrictive versus restrictive, defined by left atrial hypertension on pulmonary venous Doppler and/or an intact interatrial septum. Results: Of 73 total fetal patients identified, 49 were live-born. Survival at 2years was 29/35 [83% confidence interval (CI): 59.5%-88.9%] for the nonrestrictive group and 6/14 (43% CI: 17.7%-6.0%) for the restrictive group (p<0.0001). Of those who underwent stage 1 palliation (35 with nonrestrictive and 10 with restrictive atrial septa), both groups had a similar incidence of preoperative acidosis and need for ventilation and inotropic support. Postoperatively, there was no difference between groups in ventilator days, length of stay, or survival to discharge. There was decreased survival at 2years in the restrictive group, 60% (CI: 26.2%-87.8%) versus 83% (CI: 66.4%-93.4%) in the nonrestrictive group. Furthermore, a disproportionate number of interstage deaths was evident in the restrictive group. Conclusions: Prenatal presence of any degree of atrial septal restriction in the setting of HLHS confers a significant survival disadvantage, with increases in both early and late mortality.