The microbiota is a crucial modulator of the immune system. Here, we evaluated how its absence or reduction modifies theinflammatory response in the murine model of experimental autoimmune uveoretinitis (EAU). We induced EAU in germ-free(GF) or conventionally housed (CV) mice and in CV mice treated with a combination of broad-spectrum antibiotics either fromthe day of EAU induction or from one week prior to induction of disease. The severity of the inflammation was assessed by fundusbiomicroscopy or by histology, including immunohistology. The immunophenotyping of T cells in local and distant lymph nodeswas performed by flow cytometry. We found that GF mice and mice where the microbiota was reduced one week before EAUinduction were protected from severe autoimmune inflammation. GF mice had lower numbers of infiltrating macrophages andsignificantly less T cell infiltration in the retina than CV mice with EAU. GF mice also had reduced numbers of IFN- and IL-17-producing T cells and increased numbers of regulatory T cells in the eye-draining lymph nodes.These data suggest that the presenceof microbiota during autoantigen recognition regulates the inflammatory response by influencing the adaptive immune response