In order to identify corresponding amino acid sequences (pentapeptides) between the SPs, MPs and NPs of human coronaviruses and human autoantigens targeted in autoimmune endocrinopathies, and for a comparative analysis of the various coronaviruses proteome and the proteome of human, the original computer program was used. Quantitatively, SP, MP and NP of the human coronaviruses were found to share totally 117 minimal immune pentapeptide epitopes: 79 in SP, 14 in MP and 24 in NP, – with 18 autoantigens expressed by human endocrinocytes. The shared pentapeptides belong to the proteins of human endocrine cells. Samples of the pituitary, adrenal and thyroid from patients who died from coronavirus infection (COVID-19) were studied morphologically using histochemical methods. A high incidence of SARS-CoV-2 infection of endocrine cells was showed. The high affinity of SARS-CoV-2 the cells of the adenohypophysis was revealed, but there was no expression of viral proteins by the cells of the neurohypophysis. The foci of lesions in endocrine organs contained abundant lymphocytic infiltrates which may indicate the impact of autoimmune processes. Autoimmune disorders have a multi-faceted etiology and depend on polygenic predispose and additive action of many epigenetic and environmental factors causing hyperstimulation of imperfectly functioning immune system. It means that the phenomenon of molecular mimicry cannot be blamed as their single prerequisite, but it is just a tile in mosaic of autoimmunity. The facts revealed emphasize the need of endocrinological diagnostic alertness of a physician while observing patients with post-vaccination and post-COVID-19 health disorders.