Heparin-induced thrombocytopenia (HIT) is a heparin-dependent antibody-mediated platelet activating syndrome frequently accompanying thrombocytopenia, thromboembolism. We experienced a case of cardiopulmonary bypass using hirudin, a direct thrombin inhibitor, in a patient with HIT. The patient who showed thrombocytopenia and thrombosis after heparin re-exposure was highly suspected of having HIT. Hirudin was used in this case as an anticoagulating agent during cardiopulmonary bypass (CPB) to prevent serious complications of heparin. Hirudin 0.3 mg/kg was mixed with a priming solution of CPB and a 0.2 mg/kg IV bolus followed by a continuous infusion of hirudin 0.15 mg/kg given for anticoagulation. After CPB, forced diuresis and platelet transfusion was performed and the patient was recovered without complication.