Proteins of the complement system limit the expression of systemic autoimmunity by raising the threshold for negative selection and, in their absence, autoreactive lymphocytes seem to enter the periphery. On the other hand, complement activation in the course of systemic autoimmunity leads to tissue injury in a number of ways including direct lysis of cells, modification of cell function and by contributing to the formation of immune complexes. Excessive complement activation as a result of a regulator component deficiency leads to tissue injury that mimics that seen in autoimmune disease. Complement activation occurs during tissue injury and contributes in a major way to the expression of pathology. It appears that natural antibodies represent an early culprit in tissue injury following ischemia/reperfusion injury. Natural antibodies and probably autoantibodies present in sera of patients with systemic autoimmune disease bind to tissues already exposed to a damaging insult, activate complement and produce pathology.