Review of autopsies of 28 children with severe combined immunodeficiency (SCID) or combined immunodeficiency (CID) and three with DiGeorge syndrome showed a high incidence of acute graft-versus-host disease (GVHD) in the pancreas. Acute GVHD (seven cases: four SCID, two CID, and one DiGeorge syndrome) was characterized by lymphocytes around large to medium ducts, damage to ductal epithelium (focal necrosis, reactive nuclear changes, inspissated secretions in duct lumens), and periductal edema. Changes were judged indeterminate but suspicious for GVHD when ductal damage was slight (six cases: three SCID, two CID, and one DiGeorge syndrome). All patients with pancreatic GVHD had received allogeneic bone marrow, fetal liver or thymus transplant, or nonirradiated blood products and had evidence of GVHD in other organs. Immunoperoxidase stain for HLA-DR showed strong-to-moderate staining of duct epithelium in two of four GVHD cases for which blocks were available. This change was nonspecific; weaker staining for HLA-DR was seen in cases with nonspecific abnormalities and in viral pancreatitis. Four cases had histological evidence of viral infection: two had cytomegalovirus pancreatitis, one had patchy parenchymal necrosis caused by adenovirus, and one had giant cell pancreatitis caused by parainfluenza virus. Mild nonspecific changes, such as focal fat necrosis or acinar dilatation, were seen in seven cases. One case had unexplained marked pancreatic atrophy and fibrosis. Acute pancreatic GVHD is not uncommon in autopsies of children with congenital immune deficiencies with GVHD of other organs; however, this finding may not have strong clinical implications in this group of patients. Careful attention to pancreatic ducts is necessary for diagnosis. Unusual viral pancreatitis may also be seen in this group, as well as nonspecific abnormalities.