In this study, our objective is to compare the efficacy of the IFA and EIA methods in the detection of anti-nuclear antibodies (ANA) and anti-double stranded DNA (Anti-dsDNA) in patients with prediagnosed as systemic lupus erythematosus (SLE). All serum samples (n:59) obtained from patients with prediagnosed SLE and submitted to the Microbiology and Clinical Microbiology Laboratories between July 2005 and 2006 were examined by indirect fluorescent antibody (IFA) and enzyme immunoassay (EIA) tests and results were compared. The IFA test gave a positive ANA indication in 50 (84.7%) out of 59 patients, compared to 35(59.3%) with the EIA test. In terms of Anti-ds DNA existence, the IFA test gave a positive indication for 21 (35.6%) out of 59 patients whereas, using the EIA method, the number was 30 (50.8%) patients. We determined that the sensitivity of the EIA test to the presence of ANA was 70 %, and that its specificity was 100 %. We found that, in terms of ds-DNA existence, its sensitivity and specificity were 90.5% and 71.1%, respectively.