An 80-year-old woman with essential thrombocythemia was diagnosed with severe mitral regurgitation and moderate tricuspid regurgitation. Preoperatively, she had been treated with hydroxycarbamide and low-dose aspirin since her platelet count was high( 96.2×104/μl). After the platelet count was reduced to 46.2×104/μl, she underwent mitral valve repair and tricuspid valve annuloplasty. Atypical heparin resistance was noted intraoperatively. After initial heparin infusion, the activated clotting time(ACT) increased as expected. However, it decreased after initiation of cardiopulmonary bypass, despite additional heparin infusion and heparin concentration maintenance. A correlation between platelet factor 4 and heparin resistance was suggested. On discharge, she had no complications. We should consider the possibility of heparin resistance in essential thrombocythemia even when platelet count is adequately controlled.