Since 1943, cases of sensitization or allergy to soy-based formulas (SBFs) have been described without any consensus on their real prevalence. We identified the adjusted prevalence of IgE-mediated soy allergies in children and performed a secondary analysis of the impact of age (less than and more than 6 months). We performed a systematic review with meta-analysis of studies published from 1909 to 2013 in PubMed, Embase, LILACS, ARTEMISA, Cochrane, Bandolier, DARE and the GRADE system for grading quality. Results are presented in tables and graphs using a forest plot. The 40 studies identified established weighted prevalence of soy allergies of 0 to 0.5 % (0.27) for the general population, 0.4 to 3.1 % (1.9) for the referred population, and 0 to 12.9 % (2.7) for allergic children. Prevalence of sensitization after the use of SBFs is 8.7 and 8.8 %, depending on the method used. The prevalence of allergies to soy and IgE sensitization to the use of SBFs is less than reported. Not enough evidence exists to show a higher risk of allergy in infants younger than 6 months. The concern about soy allergy is no reason to postpone the use of SBFs in IgE-mediated cow's milk allergy infants until the age of 6 months.