The advent of cell therapies, mainly based on the use of mesenchymal stromal cells (MSCs), represents a great step forward in the treatment of immune-mediated conditions. Here, we focus on those intestinal disorders wherein MSCs have been applied for immunotherapeutic purposes and whose results are available. By virtue of their ability to favour both tissue regeneration and immune tolerance, together with a substantial lack of immunogenicity, MSCs have gained huge attention in the last decade. Following abundant positive experimental data, a sizable number of clinical trials using MSCs as a new treatment in chronic inflammatory intestinal diseases were carried out with promising results and several are still ongoing. The main indication was refractory Crohn's disease wherein both feasibility and safety clearly emerged when treating the luminal phenotype with intravenous infusion/s, albeit no definitive conclusion on efficacy may be drawn. By contrast, the availability of robust demonstration also on the efficacy when treating the fistulizing phenotype through local injection/s of MSCs has led to approval of the marketing of an industrial preparation (darvadstrocel). Successful clinical implementation of this attractive option is hampered by a number of obstacles arising from methodology and regulation issues, which require the institution of interdisciplinary task forces before this cell therapy becomes a bedside reality.