Filaggrin is one of the most important structural proteins in the stratum corneum of the human’s epidermis. There are known over forty mutations in the filaggrin gene (FLG) of which the null-type mutations such as R501X and 2282del4, localized in exon 3 of this gene, are the most significant risk factors for the development of allergic diseases. The atopic diseases develop in mucosal surfaces such as the gastrointestinal tract, the respiratory tract and the skin. We focus on research characterizing the filaggrin-deficient epidermis with respect to genetic, immunologic and microbiome abnormalities to show the consequences of these mutations in the development and progression of atopy. A case of a 3-year-old girl with food allergy, atopic dermatitis and Staphylococcus aureus infection, which was found by the presence of R501X mutation in the filaggrin gene. The girl remains under strict medical control and is subjected to integrated therapy of allergic diseases.