Gastro-intestinal cytomegalovirus infection (GI-CMV), which occurs after allogeneic stem cell transplantation (allo-SCT), is diagnosed by immunostaining of biopsied tissues obtained using a fiberscope. However, the sensitivity of this pathological diagnostic test is poor. We evaluated the suitability of using quantitative polymerase chain reaction (qPCR) to test GI-mucosal tissues for CMV. We analyzed adult patients who had undergone allo-SCT at our institute. Twenty-seven specimens were collected from patients undergoing GI-fibers-copy for upper GI-symptoms after allo-SCT. Of these patients, 9 tested positive for CMV by qPCR; their symptoms resolved soon after receiving antiviral therapies for CMV. Pathological procedures detected GI-CMV in only 3 cases. In contrast, CMV qPCR was positive for 12 of 30 specimens collected from patients with lower GI-symptoms by using colon fibers-copy. Antiviral therapies were effective in all but one case. GI-CMV was diagnosed pathologically in only 5 cases. Therefore, CMV qPCR is effective for early therapeutic intervention in CMV-GI patients after allo-SCT.