Advances in the management of hypoplastic left heart syndrome (HLHS) have resulted in improved survival. However, short and long-term mortality in patients with a restrictive atrial septum remains high. All neonates diagnosed with HLHS from 2003 to 2010 at our institution were evaluated. Patients who underwent atrial septostomy within the first 72 h conformed the restrictive atrial septum group (HLHS-RS). Patients with a non-restrictive communication (HLHS-NRS) formed the control group. Outcomes and survival status were determined from review of medical records. Of the 141 newborns diagnosed with HLHS, 20 (14 %) required intervention for a restrictive atrial septum. Procedural success was achieved in 17/20 (85 %) patients. Complications occurred in ten procedures, two of which were life threatening. No procedural deaths occurred. Overall median follow up was 35.5 months (0.4–104). Initial hospitalization survival was 16/20 (80 %) for the HLHS-RS group and 114/121(94 %) for the HLHS-NRS (p = 0.028). Twenty (14 %) patients were lost to follow up and 9 (6 %) underwent heart transplant. Overall survival was 10/16 (62 %) for HLHSRS patients and 77/95 (81 %) for HLHS-NRS (p = 0.1). Survival after initial discharge was 10/12 (83 %) for the HLHS-RS group and 77/88 (87 %) for the HLHS-NRS (p = 0.67). No predictors for HLHS-RS outcome were identified. Mortality at first-stage palliation in HLHS neonates with a restrictive atrial septum remains higher than in those with an unrestrictive communication. However, survival after initial hospital discharge is similar.