Although soy is considered to be beneficial for various health problems, including postmenopausal symptoms, osteoporosis, lipid metabolism, and obesity based on several human studies, the effects of soy intake on human health remain controversial. Soy contains isoflavones such as genistein and daidzein, which can act as weak estrogens, at least in vitro. Daidzein is metabolized into another isoflavonoid, called equol, by the intestinal bacteria in most animals and in some humans. Equol-producing bacteriotypes in individual intestines may play an important role in the various effects of soy, including the endocrine effects. Recent studies indicate that the equol and equol-producing bacteriotypes are key factors in the soy-related health benefit. Equol could be useful as a nutritional supplement. Here we review the nature of equol and the effects of equol intervention on human health.