Interest in probiotic research and its potential benefits in infant foods are relatively recent but significantly increasing. The evolution of the knowledge in the last 20 years demonstrated that alterations in the microbiome may be a consequence of events occurring during infancy or childhood, including prematurity, cesarean section, and nosocomial infections. Several pieces of evidence prove that a “healthy” intestinal microbiota facilitates the development of immune tolerance. Interventional studies suggest that probiotics could be protective against the development of many diseases. Nevertheless, many factors complicate the analysis of dysbiosis in subjects with food allergy. Comparison in-between studies are difficult, because of considerable heterogeneity in study design, sample size, age at fecal collection, methods of analysis of gut microbiome, and geographic location. Currently, there is no positive recommendation from scientific societies to use pre- or probiotics for treatment of food allergy or other allergic manifestations, while their use in prevention is being custom-cleared. However, the recommendation is still based on little evidence. Although there is valid scientific evidence in vitro, there is no sufficient information to suggest the use of specific probiotics in allergy and asthma prevention.