Heparin is clinically administered mainly by intravenous injection because of its highly hydrophilic property. A slightly hydrophobic heparin derivative which can be dissolved in organic solvent can be widely used in polymeric devices for clinical applications. In this study, hydrophobic heparin derivatives were prepared by coupling heparin with deoxycholic acid, cholesterol, lauric acid, and palmitic acid, respectively. The hydrophobicity of these heparin derivatives depended on the feed mole ratio of heparin to hydrophobic agents, and they showed good solubility in the co-solvent of acetone and water, as well as in water alone. Also, these heparin derivatives showed high anticoagulant activity. This approach for preparing hydrophobic heparin is expected to advance the drug delivery system by further extending the applications of heparin to medical devices such as cardiopulmonary bypass circuits, heart lung oxygenators, and kidney dialyzers.