Soybeans have long been recognized as an excellent source of high-quality protein. The soybean also contains a wide variety of chemical compounds that have potent bioactivity. Among these compounds are the isoflavones and the saponins. The goal of our research was to quantify isoflavone and saponin concentrations in elite soybean cultivars grown in different environments and to identify a naturally occurring high and low variety that could be used in animal studies of colon cancer. We observed significant environment x genotype interactions for the cultivars and selected 2 that provided the range of concentration for isoflavones and saponins. These were grown in an adequate quantity for animal studies, which are ongoing. We explored the influence of isoflavones and saponins on human colon tumor cells in culture, Caco-2, to determine potential mechanisms through which these compounds influence the carcinogenic process. We observed the inhibition of Caco-2 cell proliferation by isoflavones and saponins, suggesting a protective effect of these compounds in colon cancer. Using purified soy saponins, we found no negative effects on mouse growth, organ weights, or intestinal morphology when the diet contained up to 3% saponins by weight. Hence, soy isoflavones and saponins are likely to be protective of colon cancer and to be well tolerated. Continuing studies will explore the cancer-protective effects of these compounds in animal models.