In this study an universal method for preparation of biodegradable microcapsules for antigen entrapment was proposed and optimized. The multilayer microcapsules were prepared by layer-by-layer adsorption of various polyelectrolytes (such as alginate, poly-L-lysine, κ-carrageenan, chitosan and dextran derivatives). High entrapment efficiency of protein and plasmid DNA (non less than 90%) was shown. To carry out in vivo tests, a set of microcapsules with entrapped pTKShi plasmid encoding the E2 polypeptide of classical swine fever was prepared. It was shown that an injection of these microcapsules into mice induced an immune response. The highest antibody titers of mouse blood sera were got after immunization by microcapsules based on modified dextran/carrageenan and modified chitosan/carrageenan. The proposed method for antigen entrapment in biodegradable microcapsules could be used for development of encapsulated vaccines of a new generation (DNA-vaccines). © 2009 Pleiades Publishing, Ltd.