An 82-year-old woman presented with mitral regurgitation and atrial fibrillation. She was hospitalized for further examination of cardiac thrombus detected by transthoracic echocardiography. No definitive diagnosis could be made based on computed tomography and magnetic resonance imaging. Intravenous contrast echocardiography suggested a coronary sinus thrombus. Coronary angiography showed coronary sinus ostial atresia. Multislice computed tomography confirmed the presence of thrombus in the enlarged coronary sinus with coronary sinus ostial atresia and persistent left superior vena cava. Persistent left superior vena cava is present in 3% of patients with congenital heart disease. Persistent left superior vena cava is detected by chance during cardiac catheterization for other conditions in patients without cardiac malformations. The present case was detected at an advanced age, and in the absence of prior symptoms.