Lipomatous hypertrophy of the heart is a benign rare abnormality characterized by large fatty tissue deposits in the interatrial septum. An increased incidence of atrial arrhythmias is described in these patients, significant blood flow obstruction however is not the rule. We report a case of lipomatous hypertrophy of the interatrial septum, detected by transeosophageal echocardiography (TEE). The tumour mass protruded into the right atrium and the superior caval vein (SCV), thus causing upper right atrial inflow obstruction. Partial resection of the tumour and pericardial patch-reconstruction of the SCV were performed in combination with coronary artery bypass grafting due to coronary artery disease (CAD). The diagnostic and therapeutic management is discussed and a review of the literature performed.