Crohn’s colitis that does not respond to medical therapy is treated surgically with removal of the colon and rectum and creation of a permanent end ileostomy. This can be devastating for some patients and is fraught with potential surgical morbidity, and even disease recurrence in the small intestine in a third of patients. Mesenchymal stem cells target pathways of inflammation important for Crohn’s disease and are being increasingly utilized for the treatment of perianal fistulizing Crohn’s disease. We are herein delivering mesenchymal stem cells with endoscopic injection into the colon wall at the time of colonoscopy to treat inflammation of the colon and rectum related to Crohn’s disease that is not responding to medical therapy in order to avoid surgical intervention.