© 2020 Interregional public organization Association of infectious disease specialists of Saint-Petersburg and Leningrad region (IPO AIDSSPbR). All rights reserved. Relevance of the problem of a new COVID-19 coronavirus infection is obvious. Among its most important aspects that require special study, are pathogenesis and morphological changes in severe forms of the disease. Material and methods. The analysis of 18 autopsy observations was carried out. Along with routine assessment of macro - and microscopic changes, immunohistochemical studies of lungs and other organs were performed using sera against antigens CD2,3,4,5,7, 20,31,34, 56,57,69; the presence of Fe2+and Fe3+ was detected in the lungs and liver. Results. Structural changes in the lungs may be associated with cytopathic and cytoproliferative effects of the virus with damage to both the ciliary and alveolar epithelium, as well as the formation of hyaline membranes. Cellular infiltration is mainly represented by suppressor populations of T-lymphocytes and macrophages. Endothelial damage, vascular thrombosis of vessels of different calibers, and hemorrhages were detected. Many organs (lymph nodes, spleen, intestines, brain, adrenal glands) show changes that may indicate generalization of viral infection, and infiltration of CD8+ lymphocytes in the kidneys, liver, adrenal glands, pericardium, and intestines indicates a probable autoimmune component of pathogenesis. In the liver and lungs deceased from COVID-19 only small clusters of Fe3+ and Fe2+granules were detected, which can be associated (including in our control observation) with liver damage in malaria.