Biocompatibility and permeability of a microcapsule membrane governs the function of a microcapsule-shaped bioartificial pancreas. We have previously developed an alginate/sol-gel-synthesized aminopropyl-silicate/alginate microcapsule (Alg/AS/Alg), which had insufficient biocompatibility. The purpose of this study was to investigate whether the biocompatibility could improve by modifying the external surface with other anionic polymers and to investigate an influence of the modification on the permeability of the membrane. Four kinds of anionic polymers, poly(oxyethylene)diglycolic acid (3 kDa), heparin (15 kDa), Alg (54 kDa) and carboxymethylcellulose (CMC, 60 kDa) were used as the external anionic polymers. The heparin-bonded gel bead had the largest resistance to the diffusion of small molecules. The molecular mass cut-off point of 150 kDa required for immunoisolation was maintained for all anionic polymers. Cellular overgrowth to the implanted islet-enclosing microcapsule, a sign of insufficient biocompatibility, was suppressed by altering the external surface material from Alg to CMC. These results suggest that the biocompatibility of the Alg/AS/anionic polymer membrane can be improved by using a biocompatible anionic polymer. At the same time, it is suggested the influence on the permeability has to be investigated to develop an optimal microcapsule for bioartificial pancreas.