A 72-year-old woman was admitted to our department with a diagnosis of severe aortic stenosis was also diagnosed Inherited antithrombin deficiency was also diagnosed after she suffered from a pulmonary thromboembolic event 10 years previously and had been taking warfarin since then. On admission, her antithrombin activity was 53% of normal, and her PT-INR level was maintained around 2.5. Preoperative management of anticoagulation therapy included discontinuation of warfarin, and supplementation of antithrombin with heparin infusion. On the day of operation, antithrombin activity was maintained above 80% by administering antithrombin, and aortic valve replacement with a mechanical valve prosthesis was carried out under standard cardiopulmonary bypass support using heparin. Heparin infusion was continued with antithrombin supplementation until PT-INR recovered to round 2.5 with warfarin. Her intra- and postoperative courses did not show any thromboembolic events, and she was discharged 14 days after the surgery.