Drug eluting stents (DES) have dramatically decreased the rate of in-stent restenosis, which are widely used in patients with atherosclerosis. However, as research continues, increasing evidences have demonstrated that the risk of DES-related stent thrombosis (ST) has tended to increase, which is closely associated with delayed endothelium coverage. Impaired endothelium could induce platelet adhesion and aggregation, incomplete stent apposition, or neoatherosclerosis development. Thus, we will discuss the detailed mechanisms for the DES-related deendothelialization and ST, and the effects of biodegradable stents on vascular endothelium.