Soy isoflavones have been a component of the diet of certain populations for centuries. The consumption of soy generally has been considered beneficial, with a potentially protective effect against a number of chronic diseases; because of their estrogenic activity, however, negative effects of isoflavones have been postulated. This review examines the literature associated with the safety of soy isoflavones, including dietary soy isoflavone exposure data of populations with high soy intakes, human studies in which soy protein or isoflavones were provided, and toxicologic studies investigating the potential genotoxicity, carcinogenicity, and reproductive and developmental toxicity of soy isoflavones. Whereas results in some studies are limited or conflicting, when viewed in its entirety, the current literature supports the safety of isoflavones as typically consumed in diets based on soy or containing soy products.