BackgroundThe atrial intramyocardial lipomas are rare benign unusual tumors of the heart. The indication and best form of treatment for cardiac lipomas remain controversial.Case presentationThe atrial intramyocardial lipomas are rare benign unusual tumors of the heart. We report a 55-year-old Chinese female with a history of hypertension. Echocardiography and 64-slice computed tomography showed a fatty mass in the right atrium. Although she was asymptomatic, a surgical resection was indicated since the lipoma could cause an embolism and arrhythmias and its potential to enlarge. Surgery revealed an intramyocardial lipoma on the atrial free wall which was confirmed by histopathology. The patient remained asymptomatic after surgery, and no recurrence was seen after 1 year.ConclusionsAlthough cardiac lipomas are usually benign, tumor embolism, potential to enlarge, or intracardiac obstruction can cause a critical situation. Therefore, a surgical resection was indicated even in asymptomatic patients.Electronic supplementary materialThe online version of this article (doi:10.1186/s12957-015-0441-9) contains supplementary material, which is available to authorized users.