Objective The underlying mechanisms of stent thrombosis are not completely understood. Methods We experienced 12 definite stent thrombosis cases (1 early, 1 late, and 10 very late) at our hospital from July 2011 to April 2016 and evaluated the possible causes of stent thrombosis by intravascular ultrasound (IVUS). Results Five different potential morphological causes of stent thrombosis (neoatherosclerosis, stent malapposition, stent fracture, edge dissection, and stent underexpansion) were detected by IVUS in 10 cases (83.3%); in 1 of the remaining 2 cases, the discontinuation of antithrombotic drugs resulted in early stent thrombosis without abnormal IVUS findings. Of the 12 stent thrombosis cases, 4 occurred at a bare-metal stent (average time from stent implantation, 106 months); in all 12, significant neointimal hyperplasia was observed on IVUS, and 2 had plaque ruptures at an in-stent or proximal reference. Malapposed stent struts were observed in three very-late stent thromboses, and all of these underwent sirolimus-eluting stent implantation. Stent thrombosis due to mechanical (stent fracture) or procedure-related complications (edge dissection and stent underexpansion) was observed in three cases. Conclusion In patients with stent thrombosis, heterogeneous findings were observed in IVUS. This IVUS case series illustrates the possible mechanisms of stent thrombosis.