A system and method for coating an endoprosthesis involves an applicator capable of delivering a coating substance to the endoprosthesis without spraying. The applicator may have a tube or die through which a coating substance is moved upwards by capillary action or by means of a pump so as to form an accumulation of the coating substance at an upper portion of the applicator. The endoprosthesis can be lowered onto the accumulation, then axially translated or rotated in order to transfer the coating substance to selected portions of the endoprosthesis. The applicator is lowered and/or the endoprosthesis is raised in order to form gaps in the coating. Selective coating of abluminal or luminal surface of the endoprosthesis may also be performed by allowing the surface to skip on a liquid surface of a pool of the coating substance.