In autoimmune diseases the immune system attacks self antigen(s). There are more then 80 autoimmune diseases occuring in 5-6% of the population. Autoimmune diseases can be classified as systemic or organ-specific, although the basic problem with this categorization is not based on causative pathogenic factors. The diseases are diagnosed based on safe international consensus criteria. Yet, by using these criteria we miss early forms of the diseases. We follow-up the course of the disease by histological and laboratory parameters, but we miss those biomarkers, which reflect the "disease of the immune system" itself. The number of autoimmune diseases is raising, more and more diseases turn out to have autoimmune pathogenesis in the background. The better understanding of the pathogenetic background helps to divide clinical and immunological phenotypes of the disease entities, which have important diagnostic and therapeutical consequences.
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