Methods for making comb-type antithrombotic conjugate wherein substantially all side chains of water soluble poly(vinyl alcohol) (PVA) are extended by ring-opening polymerization to form a copolymer wherein substantially all terminals are conjugated to an antithrombotic molecule. In addition, a method is provided for applying a coating comprising a comb-type anti-thrombotic conjugate to at least a portion of an implantable device to prevent or reduce the formation of thrombosis on the surface of the device. A first or sub-layer of the coating is prepared by mixing a polymeric material and a biologically active agent with a solvent, thereby forming a homogeneous solution. A second or outer layer comprising a comb-type anti-thrombotic conjugate may be applied over the inner drug-containing layers using, for example, a dip coating or spray coating process. Alternatively the comb-type antithrombotic conjugate may be used as a matrix material to encapsulate a pharmaceutical agent to form microspheres or nanospheres before depositing the microspheres or nanospheres onto a medical device.