We report herein a case of a patient who suffered heparin-induced thrombocytopenia (HIT) after on-pump coronary bypass grafting (CABG). A 62-year-old woman had received coronary angiography with heparin 4 months before CABG. She had been given heparin for 7 days before CABG, and underwent the operation under cardiopulmonary bypass uneventfully. She experienced thrombosis of multiple vein grafts without deep venous thrombosis or pulmonary embolism postoperatively. During percutaneous coronary intervention for residual coronary stenoses, acute multiple thromboses in coronary stents developed. We suspected HIT and administered argatroban instead of heparin. She recovered from shock after intra-aortic balloon pump insertion and balloon angioplasty for in-stent thromboses. HIT should be suspected whenever a thrombosis suddenly occurs in perioperative cardiac patients. Early diagnosis and treatment for HIT is essential to prevent subsequent thromboembolic events.