The human digestive tract contains a large number of gut microbiota. Where the composition of the bacteria is influenced by various factors, ranging from geographical differences, to various other factors. The gut microbiota plays an important role not only in the stability of digestive function, but also in immune function, hormones, and metabolic homeostasis. Recent research results indicate that there is an autoimmune process that occurs after bacterial infection, where the mechanism involves molecular mimicry, epitope distribution, bystander activation, and cryptic antigens. The condition of dysbiosis has been associated with various gastrointestinal disorders and systemic disorders, one of which is in the group of autoimmune diseases. Increased intestinal permeability causes the flow of toxins, antigens, and bacterial metabolites from the intestine into the blood vessels. Where this condition is a hypothesis of the initiation process of autoimmune thyroid disease. A balance between protective reactions and tolerance is required to maintain intestinal homeostasis. Changes in this balance can cause auto-aggressive disturbances triggered by differences in the composition of the microbiota. The deiodinase enzyme is an important factor in thyroid hormone metabolism. Several microbes were identified as regulators of certain enzymes involved in iodothyronine metabolism. Autoimmune thyroid disease and gut microbiota have a potential relationship which, if further investigated, could be the future of autoimmune thyroid disease therapy.