A 63-year-old man was referred to our hospital because of a cardiac tumor. Transthoracic echocardiography revealed a rough, mobile tumor in the dilated right atrium, and transesophageal echocardiography showed that the tumor consisted of small, botryoidal masses. Catheter-based biopsy carried a high risk of embolism. Therefore, we used F-18-fluorodeoxyglucose positron emission tomography (FDG-PET), which revealed an abnormal accumulation in the right cervical lymph nodes, as well as in the heart. We safely performed biopsy of the lymph nodes and diagnosed the patient with primary cardiac lymphoma. We concluded that echocardiography and FDG-PET are useful for selecting an appropriate biopsy site in primary cardiac lymphoma.