Soybeans were soaked with water for 4 h, steam-cooked, inoculated with the conidia of Aspergillus oryzae, and incubated for 3 days for koji preparation. The koji was then mixed with water-soaked and steam-cooked soybeans (1:2, w/w), ground into paste, and supplemented with 15% ethanol and 12.5% NaCl or 3% ethanol and 6% NaCl for miso fermentation at 30 degrees C. Daidzin, genistin, daidzein, and genistein contents were extracted from the lyophilized and pulverized soybean powder or from the miso homogenate by a developed one-tube procedure and analyzed with an HPLC. After water soaking, daidzein and genistein contents increased markedly, whereas daidzin and genistin contents decreased. Further increases of daidzein and genistein contents and decreases of daidzin and genistin contents were observed after koji mold growth. During fermentation, fungal and lactic acid bacterial (LAB) growth in the miso products was inhibited, whereas soluble protein contents increased much more rapidly in the low-salt miso products supplemented with 3% ethanol and 6% NaCl than the other products. When the 4- and 8-week-fermented miso products were cooked with tofu for sensory evaluation, flavor ratings of the low-salt products were higher than that of a popular commercial product. In both products, the most daidzins and genistins were hydrolyzed after 4 weeks of fermentation. The hydrolytic enzymes contributing to isoflavone transformation originated from soybeans after water soaking and from koji with mold growth. It was of merit that the low-salt fermented products were fairly acceptable in flavor rating and rich in daidzein and genistein contents after 4 weeks of fermentation.