A 41-year-old man was admitted to our hospital for dyspnea on exertion and chest oppression. He was diagnosed as having pulmonary thromboembolism by pulmonary perfusion scan and angiography. An anticoagulant (heparin) and fibrinolytic (urokinase) therapy were administered to him as standard therapy. Six days after continuous infusion of heparin, however, he complained of worsening of dyspnea associated with severe hypoxemia and thrombocytopenia. Because heparin-induced thrombocytopenia was suspected, heparin administration was discontinued. Shortly after switching anticoagulant therapy from heparin to warfarin, the patient's symptom improved and his platelet count returned to the pretreatment value. In this case, it was thought that an immune-mediated response contributed to this heparin-induced thrombo-cytopenia. Moreover, we revealed platelet aggregating factor in the patient's plasma. This case illustrates that caution must be taken in the use of heparin for anticoagulant therapy in patients with pulmonary thromboembolism.