The World Health Organization has declared this century to be the century of autoimmune diseases. These include a whole spectrum of endocrine disorders, with type 1 diabetes mellitus, thyropathies, autoimmune polyglandular syndromes (APS), adrenal insufficiency and others, are among the most severe chronic non-infectious diseases in humans. Both the etiology and pathogenesis of autoimmune endocrinopathies are being actively studied, the concepts of the manifestation and progression of these diseases have already been formed, data on the genetic predisposition to one or another autoimmune damage to the endocrine system organs have been obtained, prenatal diagnosis of APD is being actively developed and introduced, attempts are being made to edit the genome in order to prevent their development. Despite this, there are still enough «white spots» in understanding the processes of induction and implementation of the mechanisms of autoimmunity in a particular person. The close connection of the immune and endocrine systems is obvious. The key question is: what is still primary, a genetic predisposition to «breakdown» of the immune system, leading to the development of an autoimmune endocrine disease, or some external influence that can cause direct damage to the endocrine organ (up to its destruction), leading in the end to the breakdown of immune tolerance and the launch of a cascade of autoimmune processes that aggravate an endocrine disorder? Modern advances not only in endocrinology, but also in immunology, molecular genetics, cell biology, etc. are absolutely necessary to clarify the relationship of immuno-inflammatory, hormonal and metabolic disorders in the pathogenesis of endocrine diseases at the cellular and molecular level and to develop new methods of prevention, early diagnosis, predicting the course and effectiveness of therapy for autoimmune endocrinopathies.