Porous affinity chitosan and chitin membranes with good mechanical strength and high protein binding capacity were prepared by using silica particles as porogen. The maximum binding capacity of affinity chitosan membrane for BSA protein is 21.8mg/mL, and that of affinity chitin membrane for lysozyme enzyme is 26.1mg/mL. Chromatographic separations of BSA and lysozyme proteins using the porous affinity chitosan and chitin membranes were performed with change of the flow rate, loading amount and concentration of protein loading solutions. Protein eluted amount and binding yield were calculated from the filtration chromatograms consisted of loading/washing/elution sequences. Protein binding amount and yield were increased with decreasing of flow rate, increasing of loading amount and concentration of protein loading solutions. Those results suggest that the porous chitosan and chitin membranes prepared by using silica particles as porogen are suitable in affinity filtration chromatography for large scale separation of proteins.