The paper presents the current data on the effect of the presence of autoantibodies on the management of autoimmune diseases: autoimmune thyroiditis, diabetes mellitus, states of carriage of antithyroid and diabetes-associated autoantibodies, 2016 algorithm for the management of pregnant women with antibodies to thyroid peroxidase, approaches to the assessment of the immune status in patients with diabetes mellitus and the presence of vitamin D deficiency, describes the impact of the correction for D-deficiency on the immune status at concomitant endocrine diseases.