A 37-year-old man had been hospitalized at another hospital where he was being treated for encephalitis. Early one morning, the patient had sudden precordial chest pain and dyspnea, so he was examined further. Contrast-enhanced CT revealed filling defects in both pulmonary arteries and in the right and left atria, indicating acute pulmonary embolism. Cardiac ultrasound revealed thrombi floating in the right and left atria, and the patient displayed pulmonary hypertension (estimated pressure : 50 mmHg). Since scattering of thrombi in the left atrium carried the risk of arterial embolism, emergency surgery was performed at this hospital. An incision was made in the right atrium with the heart stopped, revealing a tubular thrombus trapped in the foramen ovale. The trapped thrombus was completely removed, and the patient's life was saved since arterial embolism, e.g. paradoxical cerebral embolism, did not occur. This case involved a rare pathology and is thus reported here together with a discussion of the literature.