Soy protein-based formulas have been available for almost 100 years. Since the first use of soy formula as a milk substitute for an infant unable to tolerate a cow milk protein-based formula, the formulation has changed to the current soy protein isolate. Despite very limited indications for its use, soy protein-based formulas in the United States may account for nearly 25% of the formula market. This report reviews the limited indications and contraindications of soy formulas. It will also review the potential harmful effects of soy protein-based formulas and the phytoestrogens contained in these formulas.