A 61-year-old man with consciousness disorder was transferred to our hospital. Computed tomography found acute type A aortic dissection and cardiac tamponade, and an emergency operation was performed. Operation findings indicated dissection above the commissure between the left coronary cusp and the right coronary cusp, to the ostium of the right coronary. An ascending aorta replacement and coronary aorta bypass grafting were performed. The postoperative course was good, but he did not regain clear consciousness. Results of magnetic resonance imaging showed multiple cerebral infarctions. At the same time, the platelet count had decreased and we suspected heparin-induced thrombocytopenia (HIT). Following detection of an heparin-dependent antibody, administration of an heparin was discontinued. However, the platelet count still tended to decrease. Therefore, we started continuous administration of argatroban, which resulted in the gradual increase in platelet count to within normal limits on postoperative day 26. The results indicate that in patients continuously and repeatedly treated with heparin, there is a possibility of the development of HIT and thrombosis with HIT.