Miso (soybean paste), shoyu (soy sauce), sake (rice wine) and katsuo-bushi (dried bonito), which are traditional Japanese fermented foods, have been consumed for a long period of time and are considered to be the safest foods. However, fermented foods may be contaminated with mycotoxins. Fungi used for the fermentation of miso, shoyu, and sake consist of Aspergillus oryzae and A. sojae. Although A. oryzae and A. sojae belong to the A. flavus group, which is known to produce aflatoxins, none of the strains examined actually produced aflatoxins. Aflatoxin contamination of rice, miso, shoyu, sake and katsuo-bushi could not be detected. Aflatoxigenic fungi do not occur in areas with a mean temperature below 16°C. Since the mean temperature in most areas of Japan is lower than 16°C, it appears that food contamination with aflatoxigenic strains does not occur in most parts of Japan. Some koji molds are known to produce kojic acid (KA) and cyclopiazonic acid (CA). Production of KA and CA was examined and the producing strains were eliminated from the commercial fermented foods. The fate of KA and CA in shoyu fermentation was also examined and it became clear that the contents of KA and CA decreased during shoyu fermentation. Contamination of katsuo-bushi with aflatoxins, sterigmatocystin and ochratoxin A could not be detected. As mentioned previously, mycotoxin contamination, which is presently very low, should be completely eliminated in future.