Chitosan/heparin microspheres were prepared using the water-in-oil emulsification solvent evaporation technique. The microsphere diameters were controlled by selecting the fabrication process parameters. Scanning electron micrographs showed that the chitosan/heparin microspheres were regular and the surface morphology was smooth. Fourier transform infrared showed that the chitosan amino groups reacted with heparin carboxylic groups to form acylamides in the microspheres. Analysis of the microsphere cytotoxicity showed that they had no cytotoxic effect and behaved very similar to the negative control (polystyrene).To analyze the protein drug release profiles of the microspheres, bovine serum albumin was loaded as a model drug into the microspheres and released in vitro. Marked retardation was observed in the BSA release profiles. The results show that chitosan/heparin microspheres may provide a useful controlled release protein drug system for used in pharmaceutics.