Autoinflammatory diseases (AID) are genetic diseases responsible for excessive activation of innate immunity leading to blood inflammation and systemic symptoms. Most patients display digestive involvements that may resemble inflammatory bowel disease. Several studies have found dysbiosis in some AID. Gut microbiota can communicate with the host via gut-derived metabolites (Fatty acids, tryptophan, bile acids) that may have either pro-inflammatory or anti-inflammatory effects. Some metabolites can also activate the Aryl hydrocarbon receptor (AhR) pathway, which enhances gut barrier. Gut barrier dysfunction has already been associated with AID. Therfore, dysbiosis could promote digestive and inflammatory involvements in genetically predisposed patients via perturbations of gut-derived metabolites.