The human body is colonized by a large number of microbes that are collectively referred to as the microbiota. They interact with the hosing organism and some do contribute to the physiological maintenance of the general good health thru regulation of some metabolic processes while some others are essential for the synthesis of vitamins and short-chain fatty acids. The abnormal variation, in the quality and/or quantity of individual bacterial species residing in the gastrointestinal tract, is called dysmicrobism. The immune system of the host will respond to these changes at the intestinal mucosa level which could lead to Inflammatory Bowel Diseases (IBD). This inflammatory immune response could subsequently extend to other organs and systems outside the digestive tract such as the thyroid, culminating in thyroiditis. the goal of the present study is to review and analyze data reported in the literature about thyroiditis associated with IBD such as Ulcerative Colitis (UC) and Crohns Disease (CD). It was reported that similarities of some molecular bacterial components with molecular components of the host considered among the factors causing IBD through an autoimmune reaction which could involve other non-immune cell types. The axis dysmicrobism-IBD-autoimmune reaction will be investigated as a possible etiopathogenic mechanism to Autoimmune Thyroiditis. if such is the case, then the employment of specific probiotic strains may represent a useful approach to moderate the immune system.