Mitral valve replacement was performed urgently in a patient with hemorrhagic brain lesions. To decrease the risk of intracranial hemorrhage, cardiopulmonary bypass was performed using a heparin-coated perfusion system and a reduced dose of heparin. The detection of an acute intracardiac thrombus by transesophageal echocardiography during cardiopulmonary bypass exposed a potential hazard of techniques employing reduced systemic anticoagulation for cardiac operations.