Atresia of the coronary sinus orifice is rare. We describe the surgical treatment of coronary orifice atresia in an infant with a persistent left superior vena cava after total cavo-pulmonary connection for hypoplastic left heart syndrome. The diagnosis was made by cardiac catheterization after total cavo-pulmonary connection at 8 months of age. After surgery, cardiac performance deteriorated. At reoperation, the coronary sinus was fenestrated to the left atrium. The patient survived surgical treatment of coronary sinus ostial atresia unroofed to the left atrium, guiding the placement of the fenestration with a probe placed through the open cardiac end of left superior vena cava.