Inflammatory bowel diseases in children are among the most severe diseases of the digestive tract characterised by a progressive course, complications, a marked decrease in the quality of life, early disability. According to the understanding of the pathogenesis of inflammatory bowel diseases, the main components of chronic inflammatory process are disordered interrelationships, impaired immune system and genetic predisposition. Proceding from current possibilities, therapeutic activity is aimed at two pathogenetic pathways – intestinal microbiota and the immune system. The literature review presents data about the worldwide experience of using fecal microbiota transplant in children with various inflammatory diseases of the intestines. Studies conducted in patients with ulcerative colitis, Crohn’s disease, eosinophilic and microscopic colites are indicative of the efficacy and good prospects of fecal microbiota transplantation. But taking into account the microbiological and immunological heterogeneity of inflammatory bowel diseases and their only phenotypic similarity, the methods needs more detailed elaboration and creation of several treatment protocols.