Understanding of the pathophysiology of inflammatory bowel disease (IBD) is constantly evolving and, recently, a number of biologic agents that selectively target specific molecules or pathways to correct the imbalance of the gut immune system have been developed. Among them, an antibody to tumor necrosis factor (anti-TNF) is the first developed drug which has dramatically improved the management of patients with IBD. However, more than one-third of IBD patients do not respond to medications, and there is the problem of antibody formation. Therefore, enormous efforts have been made into the development of novel anti-cytokines and stem cell injection as an alternative to has been made. However, the efficacy and safety of stem cell treatment are under investigation. Some studies have reported very promising data; however, others have shown conflicting results. In addition, most trials involved a very small number of subjects and did not compare stem cell treatment with anti-TNF. The present paper reviews the function and therapeutic mechanism of stem cells for the treatment of IBD.