Soybean and soy foods are rich sources of isoflavones. Much attention has focused on isoflavonoids because of their beneficial effects on human health. Isoflavones belong to the group of phytoestrogens. Phytoestrogens are estrogenic compounds found in plants. Intestinal flora plays an important role in the absorption and metabolism of isoflavones. Some dietary components and chemical composition of isoflavones are also known to affect the absorption of isoflavones. Human metabolism and excretion of isoflavones following the consumption of soy products show considerable variation. The bioavailability of soybean isoflavones to women is dependent on gut microflora. Equol is a metabolite of daidzein produced by intestinal flora. Equol has many biological activities related to human health, and its production might be affected by compositions of diets and intestinal flora. To achieve higher production of equol from daidzein in the gut, control of the metabolic activity of intestinal flora might be of importance.