We examined changes of functional components and antioxidative activity of soybeans during the processes for producing a fermented soybean food, natto. Proteolytic hydrolysis of proteins was followed along with the changes in the contents of isoflavones, saponins, and phytic acid. The antioxidative activities were measured by radical scavenging, Fe2+ chelating, superoxide dismutase-like activity, and β-carotene-linoleic acid assay. Radical scavenging activity under hydrophilic conditions increased with protein hydrolysis during fermentation. At the same time, total isoflavones decreased. Total saponins and phytic acid were kept at similar levels. The analyses of functional components and antioxidative activities showed that antioxidative peptides generated during fermentation contributed to the total antioxidative capacity of natto.