Atg16L1 mediates the cellular degradative process of autophagy and is considered a critical regulator of inflammation based on its genetic association with inflammatory bowel disease. Here we find that Atg16L1 deficiency leads to an exacerbated graft-versus-host disease (GVHD) in a mouse model of allogeneic hematopoietic stem cell transplantation (allo-HSCT). Atg16L1-deficient allo-HSCT recipients with GVHD displayed increased T cell proliferation due to increased dendritic cell (DC) numbers and costimulatory molecule expression. Reduced autophagy within DCs was associated with lysosomal abnormalities and decreased amounts of A20, a negative regulator of DC activation. These results broaden the function of Atg16L1 and the autophagy pathway to include a role in limiting a DC-mediated response during inflammatory disease, such as GVHD. Display omitted •Mice deficient in autophagy gene Atg16l1 are susceptible to graft-versus-host disease•Autophagy-deficient dendritic cells become hyperactive following an HSC transplant•Hyperactive dendritic cells stimulate donor T cells that damage the intestine Graft-versus-host disease (GVHD) is a major complication of allogeneic hematopoietic stem cell transplantation, a procedure used to treat malignant and nonmalignant disorders. Cadwell and colleagues show that Atg16l1, an autophagy gene commonly mutated in humans, suppresses GVHD by dampening dendritic cell hyperactivation.