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The detection of antibodies to certain nuclear components has considerable importance in the diagnosis and management of patients with autoimmune diseases. In this study, antibodies to nuclear antigens in 250 positive and negative patient specimens were detected by immunofluorescence (IF) and enzyme immunoassay (EIA). Specimens were tested by three different EIA assays for autoantibodies to SS-A, SS-B, Scl-70 Sm, RNP, Jo-1, ENA, Histone, ss-DNA and ds-DNA and one IF assay for Antinuclear Antibodies (ANA). The majority of positive specimens were also confirmed positive by Western Blot. Ninety-seven percent of IF-ANA positive specimens assayed positive by EIA-ENA assay and only 6% of ENA negative specimens tested positive in IF-ANA assay indicating that EIA-ENA assay is as reliable as IF-ANA for screening patient specimens. Forty-five percent of EIA Jo-1 positive specimens showed negative IF-ANA results indicating that IF-ANA assay is not a reliable method for detection of antibodies to Jo-1. This may be due to the fact that specimens with low titer and sera which are positive for a limited number of specific nuclear antigen(s) cannot produce visible or clear fluorescence patterns and therefore are reported negative by IF-ANA. Our data shows that both methods are reliable for screening purposes, however EIA has greater specificity over IF because the presence or absence of antibody to a specific antigen can be better assessed. Overall, due to higher reproducibility, low cost, antigen specificity, and the nature of EIA, we recommend microtiter-based EIA assays for detection of antibodies to nuclear antigens.