The invention is related to a method for creating coating for medical implantable devices placed inside the recipient's body and having at least one surface contacting with blood, in particular, on blood vessel prostheses made of a polymeric material (polyethylene terephthalate), in order to activate the endothelization process and prevent thrombosis. For this purpose, the specified method is characterized by the alternation of stages of ion etching with spray coating.The proposed method allows to create a discontinuous coating on a polymer vascular prosthesis made of polyethylene terephthalate, characterized by low thrombogenicity.