A patient with myocardial failure after repair of an acute type A aortic dissection had acute heparin-induced thrombocytopenia develop during extracorporeal membrane oxygenation. Heparin was discontinued and the anticoagulant was switched to the direct thrombin inhibitor bivalirudin given with a bolus of 0.5 mg/kg followed by a continuous infusion of 0.5 mg/kg/h. Using this protocol, activated clotting time values ranged from 200 to 220 seconds. After prolonged extracorporeal membrane oxygenation support and recovery of left ventricular function, a right ventricular assist device was implanted during extracorporeal membrane oxygenation support with bivalirudin anticoagulation. For this procedure an additional bolus of 0.25 mg/kg bivalirudin was given, and the infusion rate increased to 1 mg/kg/h to achieve activated clotting time values of 300 to 350 seconds. Surgery was successfully performed with moderate intraoperative and postoperative blood loss and transfusion requirements.