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Food allergy (FA) is a major health issue for children living in Western countries. At this time the only proven treatment for FA is elimination of offender antigen from the diet. It is becoming clear that the development of gut microbiota exerts a profound influence on immune system maturation and tolerance acquisition. Increasing evidence suggests that perturbations in gut microbiota composition of infants are implicated in the pathogenesis of FA. These findings have unveiled new strategies to prevent and treat FA using probiotics bacteria or bacterial substance to limit T-helper (Th)/Th2 bias, which changes during the disease course. Selected probiotics administered during infancy may have a role in the prevention and treatment of FA. Lactobacillus rhamnosus GG (LGG) is the most studied probiotic in this field. Administration of LGG in early life have a role in FA prevention. Preliminary evidence shows that LGG accelerates oral tolerance acquisition in cow's milk allergic infants. We are understanding the mechanisms elicited by LGG and metabolites in influencing food allergen sensitization. A deeper definition of these mechanisms is opening the way to new immunotherapeutics for children affected by FA that can efficiently limit the disease burden.