Primary cardiac tumors are rarest form of cancer and the lipoma represent about 8% of these tumors. Cowden disease is a rare autosomal dominant disorder, associated to a germline mutation of the PTEN gene, characterized by multiple hamartomas and an increased risk of breast, thyroid and endometrial carcinomas. For the first time, we describe a right atrial lipoma in a patient affected by Cowden syndrome. The patient suffered of some episodes of atrial flutter. The echocardiogram showed a cardiac mass, suggestive of lipoma with cardiac magnetic resonance images. Right atrial mass was completely resected and the histological examination confirmed the diagnosis of lipoma. The patient was discharged from hospital without any complications.