Soy and its bioactive compounds, isoflavones, have become a hot issue in the last 20 years. Increased breeding of the plant has created a strong market in many countries. Nevertheless, the cross-consumption of foreign products is not safe for certain ethnic groups and requires risk assessment evaluation because of ethnic differences among populations that induce, for certain compounds, different end points in humans. For example, in Asians and white people, the intake of these compounds can have different bioactive effects. Chemically, isoflavones are isoflavonoids, a subgroup of polyphenolic compounds that have affinity for estrogen receptors and can act as endocrine disruptors in white people. Isoflavones from soy can also be found as constituents of astragalus roots, adzuki beans, chaste, green peas, chickpeas, lupins, kudzu, and red clover, among other plants. An extract named okara also contains isoflavones in variable concentrations and is a by-product of the production of soy preparations, such as tofu and soybean beverages. The main isoflavones isolated from soy are the malonyl glycosides of genistein, daidzein, and glycitein; these aglycones appear only in very low levels. All of these compounds undergo enterohepatic metabolism and are detoxicated by cytochrome P450 (CYP) 1A2 and 3A4, which imply an important potential to induce drug-herb interactions with concomitant intake. Recent research on bioactivity/toxicity of isoflavones has provided a perspective for potential health improvement, but sometimes these results are hard to compare in different ethnic groups. Correct evaluation of each extract in animal and clinical trials is the key to understanding the end points in order to assess safety. This chapter discusses, in detail, the future challenges for isoflavone-derived products, especially in the Western market.