The regularities of release of therapeutic antioxidant enzyme superoxide dismutase (SOD) from various alginate-based delivery systems (DS) into simulated gastric and intestinal fluids were determined. The following systems were used: Ca-alginate granules (AG) prepared by various methods, porous carbonate cores with multilayer polyelectrolyte coating as well as the new two-level DS (Ca-AG containing carbonate cores loaded with proteins). The influence of the method of granule preparation, composition of gelation bath and ionic composition of the simulated fluids on release profiles of the protein from different DS was revealed. SEM images demonstrated changes in DS structures in various simulated fluids. The correlation between these changes and in vitro protein release was shown. The comparison of enzymatic activity of SOD encapsulated in DS of various configurations (including the systems containing different peptidase inhibitors) was made. The efficiency of protection of SOD activity in simulated intestinal fluid with trypsin was demonstrated.