Over the third of SLE (Systemic Lupus Erythematosus) patients have a high level auto-antibodies-antigen complex that contains some complement proteins, especially C1q as the trigger protein in the classical complement activation pathway. So, the SLE, as an autoimmune disease, is certainly related to disorders caused by activation of complement system, that finally leads to tissue damage. It may also be caused by hereditary deficiency (complement genes mutations). In such case, some components of the complement system might be inactivated. There are mutations that cause disorders in each of three complement system activation pathways (classical, alternative and lectin).The serum samples of SLE patients show the presence of specific autoantibodies for some complement components. Today, for clinical management of SLE patients, determination of level of C1q-CIC and C3 complement component in serum specimens have great diagnostic and therapeutic importance. During the year 2000, we analyzed a numerous serum samples from patients suspected to autoimmune diseases (SLE especially). The samples were collected from several clinics in the Clinical Center of University of Sarajevo, mostly from Clinic of Infectious Diseases, Pediatrics, Internal Medicine and Gastroenterohepatology Clinic. Primary samples went through screening for the presence of ANA using ANA-IFA method and further characterization of ANA positive samples was carried out using IFA-ANA titration, ELISA and nephelometry.