A 72-year-old female underwent off-pump coronary bypass grafting one month after heparin exposure. Immediately after protamine administration, she developed hypotension due to acute graft failure. Grafting to left anterior descending branch was revised under intra-aortic balloon pump insertion and she was transferred to intensive care unit under stable hemodynamic condition. However, she gradually developed low cardiac output syndrome and echocardiography showed new onset of myocardial infarction. Coronary angiography on the first postoperative day revealed diffuse serious coronary thrombosis involving all grafts and grafted native coronary arteries. Emergent percutaneous coronary intervention (PCI) was performed for native vessels. Laboratory examination revealed severe progressive thrombocytopenia and she was clinically diagnosed as heparin-induced thrombocytopenia (HIT). After cessation of all heparins and alternative anticoagulation with argatroban, thrombocytopenia was improved and some of occluded grafts were recanalized. She was discharged on the 51st postoperative day. Acute graft thrombosis, especially caused by HIT, is a serious complication, which sometimes results in mortality. This is a successful case treated by PCI followed by an alternative anticoagulation.