Two patients with hypoplastic left heart syndrome had coronary sinus orifice atresia with persistent left superior vena cava. Both patients underwent successfully coronary sinus unroofing. One underwent surgery at the time of the bidirectional Glenn procedure and the other before creation of a total cavopulmonary connection. According to our population-based database, 10.3% of patients with univentricular heart have persistent left superior vena cava, and 2.3% have associated coronary sinus orifice atresia. Our cases highlight the importance of recognizing this anomaly in patients with univentricular heart to avoid high coronary venous pressure, which is potentially lethal.