We evaluated the mesh size and homogeneity of polymer network by dynamic light scattering and discussed the relationship between the physical properties of polymer network and the protein separation behavior by capillary polymer electrophoresis. We compared three kinds of sieving polymers in solutions with a wide range of molecular weights and concentrations: polyacrylamide and polyethylene oxide as flexible polymers, and hydroxyethyl cellulose as a semiflexible polymer. We found that the mobility of protein was dominated primarily by the mesh size, irrespective of the type of sieving polymers, and the peak spacing between protein peaks increased drastically in the range of xi < 10 nm, where the mobility also decreased. And the peak widths were dependent on the molecular species of sieving polymers and their homogeneity of polymer network. We proposed that a polymer network with a homogenous mesh size of less than 10 nm is the best sieving medium for separation of the proteins in the molecular weight range 14 300-97 200 Da from the view point of the resolution in protein separation.