Coronary artery bypass grafting (CABG) is an established treatment for multivessel coronary artery disease. However, problematic situations are occasionally encountered after CABG, such as disease progression in the native coronary artery with graft occlusion, which causes difficulty in revascularization. The purpose of this study was to evaluate changes in the native coronary artery after CABG. Between 2009 and 2012 in our institution, 351 patients underwent CABG, and 768 bypass grafts were anastomosed to non-occluded coronary arteries. Of these, 489 bypass grafts had available early postoperative angiographic results (≤6 months) suitable for assessment in this study. We defined malignant graft failure after CABG to be bypass graft occlusion and de novo complete occlusion of the target native coronary artery proximal to the graft anastomosis site. In the early angiographic results, 17 grafts were occluded (17/489; 3.5 %). Two of the grafts displayed malignant graft failure (a saphenous vein graft to the right coronary artery and a saphenous vein graft to the diagonal branch) (2 of 17 occluded grafts, and 2 of 489 studied grafts). Of the patent bypass grafts, 24 involved progression to occlusion in the proximal native coronary artery (19 saphenous vein grafts, 4 left internal thoracic artery grafts, and 1 right internal thoracic artery graft). Malignant graft failure was uncommon during short-term follow-up after CABG. At the same time, disease progression in the proximal native coronary artery from stenosis to occlusion following patent bypass grafting was relatively common, especially for vein grafts.