The use of stem cells in complex therapy of inflammatory bowel diseases has became perspective therapeutic strategy. Mesenchymal stem cells, which have immunomodulatory, anti-inflammatory properties and high regenerative potential, are used for therapy of inflammatory bowel disease, what is making them attractive to clinical application. According to the results of the conducted studies, mesenchymal stem cells improve clinical and microscopic manifestations of colitis, reduce system and local production of pro-inflammatory cytokines, suppress inflammatory process, stimulating tissue regeneration at the same time, promote the increase in the duration of remission of a disease, reduce the risk of the relapse of ulcerative colitis. Preliminary results of clinical and experimental studies carried out in the world justify the relevance, prospects and sufficient safety of the transplantation method of allogenic mesenchymal stromal cells of bone marrow for treatment of patients with the ulcerative colitis.