Summary: The level of knowledge about the human microbiome is constantly growing. Due to the widespread and growing trend of allergic diseases in children, the relationship of the microbiome with allergic diseases is an area of special interest. Food allergy is one of the first manifestations of atopic diseases that precede the development of the allergic march. Among the microbiome of the various studied compartments, the gut microbiome is the best known. For this reason, many researchers are trying to explain the potential relationship between food allergy and the gut microbiome, which may also soon translate into practical recommendations. This paper reviews the available results of clinical trials on the role of the gut microbiome in the development of allergic diseases, in particular food allergy, in children. Based on the results of studies on the microbiome this article also presents attempts at preventive and therapeutic interventions for food allergy.