Vascular grafts prepared from synthetic polymers have serious shortcomings that can be resolved by surface modification, such as by immobilizing heparin. In this study, the mechanical properties, biocompatibility, anticoagulation property, and water contact angle of two heparin-conjugated poly(ε-caprolactone) scaffolds (PCL-hexamethylendiamine-heparin, PCL-HMD-H. PCL-lysine-heparin, PCL-LYS-H) were compared to identify a preferred heparin conjugation method. An evaluation of the subcutaneous tissue biocompatibility of the scaffolds demonstrated that PCL-HMD-H had better endothelial cell proliferation than the PCL-LYS-H and was therefore a promising scaffold candidate for use in vascular tissue-engineering.