We evaluated two enzyme immunoassays (EIA) for detection of antinuclear antibodies (ANA) which became recently available and which were designed for application on a fully automated system; (i) the EIA-ANA screen kit from Sigma Diagnostics (St. Louis, MO, USA) applied on APTUS, an automated EIA analyser from Sigma Diagnostics and (ii) the Cobas Core Hep-2 EIA-ANA assay applied on the fully automated Cobas Core immunochemistry analyzer from Roche Diagnostics (Basel, Switzerland). The evaluation was done by an analytic comparison of the automated systems to an established indirect immunofluorescence (IF) method performed on SSA transfected human epitheloid cell substrate slides. Three hundred and thirty six samples were tested with the Sigma EIA-ANA assay and 603 samples with the Cobas Core Hep-2 EIA-ANA assay. For both EIA systems, there was a trend of generally increasing signal from the assay system with increasing IF-ANA titers. With an IF-ANA reference range of < 1:160, concordance between Sigma EIA-ANA and IF-ANA was 86% and concordance between Roche EIA-ANA and IF-ANA was 85%. When compared to IF-ANA with a reference range of < 1:160, sensitivity and specificity of the EIA-ANA screen was 0.65 and 0.92, respectively, for Sigma EIA-ANA and 0.61 and 0.91, respectively, for the Cobas Core assay. The low sensitivity observed with both methods is a major concern. Sigma EIA-ANA screen revealed the presence of autoantibodies in 23 of the 29 samples containing antibodies to extractable nuclear antigens (ENA) and/or double stranded DNA and the Cobas Core Hep-2 EIA-ANA assay revealed the presence of autoantibodies in 40 of the 43 samples containing antibodies to ENA and/or double stranded DNA.