Donor origin of epithelial intestinal cells has been studied in animals and humans after transplantation and has been used as evidence of hematopoietic stem cell (HSC) plasticity. However, in the human gastrointestinal tract, no study used X- or Y-chromosome detection by fluorescence in situ hybridization (FISH) coupled with immunologic stainings to characterize cell types on the same tissue section. Here, we combined these techniques on the same section of duodenal epithelium in 6 patients with acute graft-versus-host disease. Donor-derived lymphoid cells were detected in the epithelium and the lamina propria, as expected. However, using our stringent criteria, no donor-derived cells could be proven to be epithelial.