Autoimmune diseases are characterized by chronic course with flares and remissions leading to persistent invalidity or even death in many instances. The vital elements of these diseases are the presence of antigens that are integral components of one’s own cells, which are therefore called autoantigens, and the presence of autoantibodies produced for their elimination. Over 70 autoimmune background diseases are known currently, and it is estimated that they affect about 5% of the world population. In most cases, identification of autoantigens against which the immune response is directed has been done, but new ones are constantly being defined. In this paper we discuss the issue of mechanisms responsible for autoimmune diseases development with special focus on cellular and humoral response, immune tolerance, genetic predisposition, available treatment options and possible future therapeutic strategies.