To evaluate local cytomegalovirus (CMV) infection in patients who developed diarrhea after allogeneic hematopoietic stem cell transplantation (HSCT), histologic and molecular analysis was carried out with intestinal biopsy samples. from 17 transplant recipients. A CMV-specific intranuclear inclusion body indicating intestinal CMV disease was documented in 2 biopsy samples. CMV DNA was detected by quantitative polymerase chain reaction in 8 of 23 (34.8%) samples, including 2 samples diagnosed with intestinal CMV disease. Of 15 patients without histologic confirmation of intestinal CMV disease, pre-emptive therapy was carried out for 8 patients based on positive antigenemia, and for 2 patients on positive CMV DNA, respectively. Intestinal CMV disease was successfully treated with antiviral therapy for 2 patients and prevented with pre-emptive therapy based on either positive antigenemia or positive CMV DNA for 10 patients. Endoscopic examinations with histologic and molecular analysis may be important in the early treatment and the prevention of intestinal CMV disease in patients with diarrhea after allogeneic stem cell transplantation.