In recent years the interest in stem cell-based therapies for gastrointestinal injury has been increasing continuously. From the clinical point of view, transplantation of bone marrow derived stem cells may represent an alternative therapy for gastrointestinal injury, such as radioactive injury, inflammatory bowel disease, and other refractory gastrointestinal tract injury. There were several reports indicated that bone marrow derived stem cells located in the injured gastrointestinal tract and contributed to its regeneration by differentiating into functional epithelia cells or infusing with the gastrointestinal stem cells. Although the concept of cell-based therapy for various diseases of the gastrointestinal is widely accepted, the practical approach in humans remains difficult. Here we discussed the recent published data on clinical and experimental bone marrow stem cell transplantation and the possible role of stem cells in gastrointestinal tissue repair.