Bronchogenic cysts are classified as a type of congenital foregut cyst. They are usually extrapulmonary and occur mostly along the tracheobronchial tree. Intracardiac bronchogenic cysts are very rare. As far as we know, only 3 cases have been reported previously. This paper presents a unique case of a 70-year-old male who was diagnosed with a bronchogenic cyst in the interatrial septum with a concomitant persistent left superior vena cava. He underwent successful complete excision of the cyst under cardiopulmonary bypass and enjoyed an uneventful life with normal sinus rhythm during the 1-year follow-up. The relevant literature is reviewed and an explanation for the embryogenesis of the bronchogenic cyst in such a peculiar location is proposed.