Graft-versus-host-disease (GVHD) following stem cell transplantation (SCT) is a common complication in patients that have undergone allogenic SCT but rare in recipients of autologous SCT. Gastro-intestinal tract (GIT)-GVHD can be difficult to diagnose due to non-specific symptoms such as fever, nausea, diarrhea, and vomiting; a histological confirmation is therefore required. Here, we present the findings of a whole-body 18FDG PET/CT with extensive and multifocal involvement of the GIT in a patient that developed severe acute GVHD 93 days post autologous SCT for Hodgkin’s lymphoma. PET and CT findings included characteristic patterns of bowel inflammation with bowel wall thickening, mural stratification and enhancement with high FDG-uptake of the involved regions, as well as typical extra intestinal findings such as ascites, engorgement of the vasa recti and stranding of the mesenteric fat. Although, the above-mentioned findings are not exclusive to GIT-GVHD and can be seen in other settings of inflammatory bowel disease such as enterocolitis or Mb Crohn our findings were used for targeted biopsy that confirmed acute GIT-GVHD. This case demonstrates that 18F-FDG-PET/CT can be a valuable non-invasive tool in mapping the activity and distribution of intestinal GVHD and direct for targeted biopsies of involved regions.