Systemic lupus erythematosus (SLE) is viewed as a prototype of generalized autoimmune disease. The causes and mechanisms of inflammatory damage to various organ systems are not known. In this article, we will try to conceive a synopsis of existing hypotheses from the literature and our own data in order to project directions for further research. The use of the methods of modern biotechnology promises further insights into details of the genetic predisposition to this disease as well as into environmental factors that lead to disordered immunoregulation and organ damage.