Food allergy is the pathological response of the body mediated by the allergens present in the food products. This problem more often affects children than adults. Food allergy is classified as IgE dependent, in which IgE antibodies are involved, as well as IgE independent, which pathomechanism is not fully understood. 19–25 nucleotide miRNAs are involved in many processes, including, but not limited to, the immune response. In this paper I focused on the altered expression of miRNA-98, and on the miRNA-17-92 cluster in food allergy. The increase in expression of these molecules is associated with decreased expression of anti-inflammatory cytokine IL-10, as well as reduced expression of thrombospondin-1, which is also involved in the immune response. Galectin-1 offers the promising future goal of further research as its use in the treatment of food allergy in patients. miRNA molecules can also be assigned a protective effect on the occurrence of allergies through appropriate processing of cow’s milk.