Bronchogenic cysts in the interatrial septum are very rare. We experienced a case in which a 39-year-old man, incidentally diagnosed through echocardiography as having a cardiac tumor, was surgically treated. Pathologic investigation of the tumor, which was located in the interatrial septum and resected, revealed that the tumor was a bronchogenic benign cyst. Tumor enucleation was performed and the resultant atrial septal defect was closed by an autopericardial patch.