A stent having a multi-layered coating adhered to its surface which can prevent restenosis and thrombosis at the implant site. The stent coating is comprised of two layers. The first layer is a polymeric coating with one or more biologically active agent(s) dispersed therein. The second layer is comprised of a hydrophobic heparinized polymer that inhibits blood coagulation and provides a hydrophilic surface for reducing the friction between stent and lesion site. In preferred embodiments of the invention, the multi-layered stent is effective in deterring restenosis and thrombosis at the implant site. In these same preferred embodiments, the multi-layered stent is capable of reducing the burst release of the biologically active agents from the first layer and sustaining a release of an effective amount of these agents for a relatively extended period of time. Methods of applying the multi-layered coating to the stent surface are also part of this invention.