A mass was identified in the atrial septum by clinical imaging in a patient who had multiple large lipomas of the skin. Multislice computed tomography and magnetic resonance imaging indicated that the interatrial mass was a fatty infiltration. In order to discriminate the myocardial lesion from myxoma and other benign conditions and malignant tumors, percutaneous transvenous biopsy was performed. Microscopic examination demonstrated the cardiac mass to be lipomatous hypertrophy of the interatrial septum (LHIS), and the skin lesions, simple lipomas. The LHIS is itself a rare condition, and its development in patients having multiple ponderous lipomas, or lipomatosis, could not be found in a previous report. This may be the first published case of LHIS, which likely represents cardiac involvement of lipomatosis.