While stem cell-based treatments have been established as a clinical standard of care for some conditions, such as hematopoietic stem cell transplants for cancer, the scope of potential stem cell-based therapies has expanded in recent years due to advances in stem cell research, paving the way for the increasing utilization of stem cell therapies in severe immune-mediated diseases including inflammatory bowel diseases (IBDs) and, in particular, Crohn's disease. Both hematopoietic stem cells and mesenchymal (stromal) stem cells are considered to be of potential therapeutic benefit in immune-mediated conditions. A growing body of experimental and clinical evidence shows that hematopoietic stem cell transplant induces long-lasting remission in a majority of patients with active severe Crohn's disease refractory to drug treatments, and the differential effect of potent immunosuppression and immune reconstitution in this setting is under evaluation. Mesenchymal stem cells have been shown to exert immunomodulatory action on various types of immune-mediated diseases, and in experimental models of IBD, but evaluation of the potential efficacy of this therapy in IBD is still in the early stages.