Lipomatous hypertrophy of the interatrial septum is a rare cardiac lesion that is usually limited to the interatrial septum. We report a case of an extensive lipomatous hypertrophy, which protruded into the right and the left atrium as well as the superior and the inferior vena cava and the right ventricle. A 71-year-old woman was referred to us because of a cardiac mass on a transthoracic echocardiogram, performed on a routine check-up because of a known membranous ventricular septum defect. She underwent surgical resection of the mass and closure of the ventricular septum defect. The postoperative period was complicated by superior vena cava syndrome for which she underwent re-operation. The post mortem histopathological diagnosis was a lipomatous hypertrophic interatrial septum.