The specific relationship between the endocrine and immune systems is represented by a numerous number of factors and mechanisms that form the structure and ensure the function of each of the two systems. For example, immunocompetent cells can produce immunologically active substances, as well as some hormones. On the other hand, immune cells are available to the effects of endogenous hormones. Currently, the so-called cross-regulation of endocrine and immune mechanisms in an equilibrium of pro-and anti-inflammatory responses has not been sufficiently studied. Among other autoimmune lesions, autoimmune thyreopathy occupies a significant place. The development of an autoimmune lesion of the thyroid gland is a complex process, which is the result of the interaction of infiltrating lymphocyte and thyrocyte tissue that can express a wide range of molecules involved in the immune response. Immunological and immunogenetic factors play a major role in the pathogenesis of autoimmune thyroid diseases, such as autoimmune thyroiditis and Graves disease. Despite the fact that more than 100 years have passed since the first description of autoimmune thyroiditis and Graves disease has been known for many centuries, the mechanisms of these pathologies are still not fully understood.