The invention is directed to an implantable stent prosthesis comprising a sidewall and at least one channel for containing a biologically active material. A method for making such stent prosthesis is also disclosed. In the method, at least one tube or mandrel is placed in contact with a covering material on a stent and surrounded by the covering material to form a channel. Alternatively, a channel can be formed by covering the tube or mandrel with a channel material and exposing the covered tube or mandrel to an appropriate treatment. The channel can be attached to a sidewall of a stent or attached to a strut material to form a stent wire. A method of treating an afflicted area of a body lumen by implanting the stent prosthesis is also disclosed.