Acute graft-versus-host-disease (aGvHD) is a typical complication after allogeneic hematopoetic stem cell transplantation (ASCT). About 30-60% of patients after ASCT are affected by aGvHD, which constitutes a relevant burden of morbidity and mortality in these patients. Fecal microbiota transplantation (FMT) is a therapeutic concept to treat intestinal dysbiosis of various origin by infusion of the stool microbiota of a healthy donor into the gastrointestinal tract (GI) of a patient. FMT can be performed endoscopically by colonoscopic deployment of the donor microbiota into the patient´s caecum and terminal ileum. Patients with gastrointestinal aGvHD (GI-aGvHD) are known to comprise a significant dysbiotic colonic microbiota that can be attenuated by FMT.