SummaryThe incidence of autoimmune diseases in industrialized countries is constantly increasing over past decades. These diseases lead to increased mortality and persistent reduction in quality of life of the patients, posing a severe medical burden. Treatment of autoimmune diseases is often based on unspecific immune suppression, increasing the risk of infectious diseases as well as cancer manifestation. Pathogenesis of autoimmune conditions is complex and includes not only genetic factors, but also environmental influence, which is considered to be the reason for the rise of incidence of autoimmune diseases. Environmental factors comprise numerous elements, such as infections, smoking, medication, diet etc., which can either promote or prevent the onset of autoimmunity. However, the mechanisms of environmental influence are complex and for this moment not clearly understood. Deciphering of these interactions could enhance our comprehension of autoimmunity and provide some novel treatment options for the patients.