Cytomegalovirus(CMV) colitis is an important opportunistic infection in immunocompromised individuals. The clinical symptoms are abdominal pain, diarrhea, colonic hemorrhage and perforation. The endoscopic appearance shows three characteristic features with focal or diffuse inflammatory changes, submucosal hemorrhagic spots, and well demarcated ulcers. We experienced a case of CMV colitis in an 8-year-old girl presented with Stevens-Johnson syndrome, vanishing bile duct syndrome and infection-associated hemophagocytic histiocytosis, which developed during chemotherapy with etoposide and dexamethasone for hemophagocytic syndrome. The impaired immunity caused by chemotherapy is the most likely possible cause of CMV colitis in this case. We confirmed this case by endoscopic findings, the presence of cytomegalic cells on mucosal biopsy specimens, immunohistochemistry with monoclonal antibody to CMV antigen, and serologic study, and report with a brief review of the literature.