Soy-protein formulas are widely used for feeding babies with cow-milk allergy. When they first were marketed, these formulas were the only available cow-milk substitute and they ensured a normal life for many children who were affected by the large spectrum of clinical manifestations of cow-milk allergy. Soy-protein formulas were also given to allergy-prone infants for the prevention of atopic diseases when breast milk was not available. Several researchers studied the prevalence of soy sensitization in allergic disease. Few studies used a challenge test for the diagnosis of soy allergy, even those in patients in whom soy allergy was suspected. In most studies the diagnosis of soy allergy was based on anecdotal case histories reported by parents and was not substantiated by scientific diagnostic criteria: no challenge test to soy was made nor were data available on specific immunoglobulin E to soy. In this paper we critically reviewed literature on the safety of feeding soy-protein formulas to babies with cow-milk allergy as well as on the prevention of cow-milk allergy.