Atopic diseases of infants and children are common, debilitating, chronic and sometimes even life-threatening. Several well-conducted studies in high risk babies have demonstrated a significant reduction in the prevalence and severity of atopic diseases with dietary and environmental manipulations. The currently available cow's milk (CM) substitutes for infants are soy protein (SP) formulas (SPFs), hydrolyzed formulas (HF), and home-made meat-based formulas. Soybeans have been cultivated in Eastern countries for many centuries and were first used to feed US babies with CM allergy (CMA) in 1929. Since then, SPFs containing purified SP, a mixture of vegetable oils, and purified carbohydrate have been developed. From a nutritional point of view, SPFs are adequate, support normal growth, protein status, bone mineralization, are well accepted, and economical. SPFs are used for different conditions including CMA, lactose and galactose intolerance and in the management of severe gastroenteritis, and some studies show that feeding SPFs for the first six months of life significantly reduces the prevalence of atopic diseases in high risk babies. Although gastrointestinal symptoms and atopic dermatitis (AD) may occur in some SPF-fed children, anaphylaxis following the ingestion of soybean is extremely rare in children. However, in the past few years the antigenicity/allergenicity of SPFs has been over-emphasized in the medical literature. In this paper on the natural history of soy antigenicity/allergenicity we discuss all the pros and cons of SPFs, their composition and nutritional value, the basic immune definitions, chemistry and characterization of SPs. We then discuss the antigenicity and allergenicity of SPFs in animals, recent data on the use of SPFs and the incidence of soy allergy in children, clinical reactions to SPFs, and the clinical relevance of skin testing and IgE antibodies to soy, challenge test procedure, clinical indication of SPFs, and their relevance in the prevention of atopy. We have meta-analyzed 17 different studies and conclude that history-based SPF allergy incidence totals 27%, in skin prick tests (SPT) RAST-oral food challenge (OFC)/double-blind food challenge (DBFC)-based epidemiological studies attains 3%, and in challenge test studies 4%. We suggest that double-blind placebo-controlled food challenge (DBPCFC) studies in larger cohorts of babies may establish a more reliable prevalence of SPF allergy in different disorders associated with CMA.