Review of the literature is devoted to the study of the pathogenesis of SARS and influenza, the severity of clinical symptoms which are largely determined by the degree of activity of immune reactions host. Severe and complicated forms of influenza and SARS are developing against a background of reducing the functional activity of natural killer cells, phagocytic and metabolic activity of peripheral blood neutrophils, the presence of interferon deficiency.. Activation of lipid peroxidation, which leads to a loss of barrier function of cell membranes a major cause of the generalization of a viral infection and cytokine storm is the trigger for the development of systemic inflammatory response syndrome with the risk of formation of multiple organ dysfunction syndrome.