The purpose of this study was to evaluate the precision and accuracy of a commercial multiplexed kit for the measurement of 9 anti-nuclear antibodies (ANAs; anti-SS/A, anti-SS/B, anti-Sm, anti-RNP, anti-Jo-1, anti-Scl-70, anti-dsDNA, anti-Centromere B, and anti-Histone), and to compare these results to a subset of ANAs measured by enzyme-linked immunosorbent assays (ELISA) and immunodiffusion (ID). Sera were obtained from 22 systemic lupus erythematosus (SLE) patients, twelve controls and five others (commercial source) with various autoimmune diseases. ANA results from the AtheNA MultiLyte ANA II Assay (AtheNA) were compared to ELISA results (controls) and patients (ID). The AtheNA interassay coefficients of variation (CVs, N = 39, performed in duplicate; replicated 3x) ranged from 6.2% to 16.7% (mean = 9.8%), while the intra-assay CVs ranged from 5.8% to 14.3% (mean = 10.8%). Compared to results for SLE cases and controls, the sensitivity of AtheNA ranged from 85.7% to 100% (mean = 97.1%), while diagnostic specificity ranged from 16.7% to 100% (mean = 71.6%). There was significant agreement (P values ranging from 0.0001 to 0.03) when analytes coanalyzed by AtheNA and ELISA/ID were evaluated using Cohen's kappa (kappa values ranging from 0.376 to 1.000). No false positive ANA results were observed for either the control or commercial source autoimmune disease sera. These results indicate that the AtheNA assay is a precise and accurate alternative for performing multiple ELISAs or IDs in the diagnosis of autoimmune diseases, especially when the number of sera to be tested is large, such as in clinical screening or epidemiologic studies. It also appears that the AtheNA assay identifies positive ANA specificities which are missed by ID techniques, suggesting that it may have greater analytical sensitivity for some ANAs.