Soy protein has been used in infant feeding in the West for nearly 100 y. Soy protein infant formulas have evolved in this interval to become safe and effective alternatives for infants whose nutritional needs are not met with human milk or formulas based on cow's milk. Modern soy formulas meet all nutritional requirements and safety standards of the Infant Formula Act of 1980. They are commonly used in infants with immunoglobulin E-mediated cow's milk allergy (at least 86% effective), lactose intolerance, galactosemia, and as a vegetarian human milk substitute. Largely as a result of research in animal models, concerns have been voiced regarding isoflavones in soy infant formulas in relation to nutritional adequacy, sexual development, neurobehavioral development, immune function, and thyroid disease. We discuss the available clinical evidence regarding each of these issues. Available evidence from adult human and infant populations indicates that dietary isoflavones in soy infant formulas do not adversely affect human growth, development, or reproduction.