The human digestive tract is inhabited by hundreds of bacterial species, both aerobic and anaerobic, bacteriophages, viruses and fungi that collectively are referred to as intestinal microbiota. Microbiota has a significant impact on the production and maintenance of immunological, hormonal and metabolic homeostasis. Dysbiosis is present in inflammations, e.g. intestinal inflammation, autoimmune diseases, e.g. multiple sclerosis, type 1 diabetes, rheumatic diseases, metabolic disorders such as obesity or type 2 diabetes, and mental illness. Currently, numerous studies are underway on the effect of microbiota on thyroid autoimmune diseases. . It seems, that microbiota has a small, if any, effect on the metabolism of iodine and selenium - elements particularly responsible for thyroid homeostasis. However, the relationship between thyroid function and the gastrointestinal tract has been proven