Pigmented rice is the rice grain having red, black, or green color in its outer covering layers. Koji is a culture product of filamentous fungi on cereal, and has been widely used for fermenting various foods and beverages in East-Asia. We investigated whether these pigmented rices could be used as a substrate for Aspergillus strains and Rhizopus strain to produce koji. The glucoamylase activities of the bara-koji from the pigmented rices were lower than that from white rice. However, the acidic protease and antioxidant activities of the koji from the pigmented rices were higher than that from white rice. Therefore, the koji from the pigmented rices has a potential to create novel fermented foods.