Bioabsorbable polymer scaffolds with coatings are disclosed that include immobilized antithrombotic agents on the scaffolds or in or on the coatings. The agents act synergistically with antiproliferative agents released from coatings by providing hemocompatibility during and without interfering with antiproliferative agent release. Methods of modifying scaffolds and coatings with the antithrombotic agents are disclosed.