Allergy tends to occur more rarely among members of larger families, where infections occur in childhood. This intuition was called “Hygiene Hypothesis”. With the discovery of the microbiota, this hypothesis was reformulated in the “Microflora hypothesis of allergic disease”. Controversial data have emerged from intestinal microbiota evaluation in food allergy. Studies based on the creation of large birthcohorts will be needed to identify and possibly correct the dysbiosis associated with the appearance of food allergy.