Distribution of bovine serum albumin and ferritin inside polyelectrolyte microcapsules was studied by transmission electron and confocal microscopy at the pH range 2-5. It was estimate that protein's distribution depends on isoelectric point (pI) and first polyelectrolyte used for preparation of capsule shell. So peptide is placed in the bulk of capsule if pH values of medium are lower isoelectric point of protein and polycation was used as a first polyelectrolyte layer. If the first polyelectrolyte was polyanion, the protein is located near internal surface of the shell. The protein is situated near internal surface of the shell for both polyelectrolytes when pH is equal to pI.