We examined the dietary intake and sources of isoflavones (daidzein and genistein) among Japanese subjects based on dietary records (DRs). The subjects comprised two groups: 1,232 who completed one-day DRs (Group 1) and 88 men and women who kept four four-day (16-day) DRs. For quantitative data on the level of daidzein and genistein in soy foods, we extensively reviewed the literature, particularly for Japanese soy foods, and adopted the median value for each food. The median intake of daidzein was 12.1 and 9.5 mg/day among Groups 1 and 2, respectively, while the corresponding values for genistein were 19.6 and 14.9 mg/day. The top four foods (tofu, miso, natto, and fried tofu) covered about 90% of the population intake of daidzein and genistein. It did not seem feasible to estimate one's intake of isoflavones by using dietary recording/recall in epidemiological studies, since the day-to-day variation in intake was too large, the within-person coefficient of variation being 89.1% for daidzein and genistein. Therefore, we should use other methods, such as food-frequency questionnaires, focusing on the four major sources of isoflavones, to assess individual isoflavone intake.