Gastrointestinal (GI) GVHD after allo-SCT is diagnosed on the basis of symptoms and findings in endoscopic mucosal biopsy specimens. However, GI symptoms often persist despite treatment and whether a second endoscopy may be helpful in determining the most suitable therapy is not established. We identified 31 patients with persistent diarrhea who underwent more than one endoscopic study. All cases underwent serial microbiological stool analysis and CMV-detecting assays on serum and biopsies. Of the 31 initial GI biopsies, 20 (64.5%) were classified as GVHD, two (6.5%) as GVHD with CMV, four (13%) as non-CMV infection, and five (16%) as normal or unspecific. The second GI biopsies were diagnostic of GVHD in nine cases (29%), GVHD simultaneously with CMV infection in four (13%), regenerative changes post-GVHD in five (16%), CMV infection in four (13%), and normal or unspecific in nine (29%). In 22 of the 31 patients (71%), the histological findings of the second/third endoscopic biopsies differed from the findings of the first endoscopy and led to a therapy change in 77%. In conclusion, serial GI endoscopies are of reliable diagnostic value and can impact on therapeutic decision-making for patients with persistent diarrhea after allo-SCT.