GI perforation after stem cell transplantation is extremely rare and is associated with poor prognosis. In addition, the clinical limitations of MMF are associated with GI intolerance and hematologic suppression. However, the exact mechanism whereby MMF induces changes in GI mucosa is unknown. Currently, there is no definite method to distinguish between GI toxicity associated with MMF and GVHD. It is important to recognize association between MMF and the histologic changes mimicking GVHD, given that GVHD is a significant differential diagnosis in stem cell transplant patients. MMF-induced colitis and GI perforation are extremely rare but should be considered in patients presenting with diarrhea and abdominal pain. Histology and clinical features are helpful to distinguish this condition from ischemic colitis. Early recognition of GI perforation is necessary for proper diagnosis and subsequent intervention. Emergency medical treatment and laparotomy have been shown to reduce the risk of fatal complications in patients presenting with GI symptoms suspected of GI perforation.