We set out to determine the agreement of three multiplex immunoassays for the detection of autoantibodies involved in connective tissue disease using clinically defined sera. Usefulness of the immunoassays will be defined by correlation to disease state. Using the immunoassays from Inova Diagnostics, Biomedical Diagnostics (BMD), and AtheNA, reactivity, to Smith (Sm), ribonucleic protein (RNP), SSA (Ro), SSB (La), Scl-70, and dsDNA or chromatin, we tested 273 clinically defined sera consisting of 57 systemic lupus erythrematosus (SLE) sera, 69 rheumatoid arthritis (RA) sera, 47 sera defined as various other connective tissue diseases, and 100 normal donor sera. Samples were also tested for anti-nuclear antibody (ANA) oN HEp-2 cells by IFA for analysis of discrepant results. Inova, BMD, and AtheNA assays demonstrated 57%, 89%, and 80% concordance, respectively, in the 47 connective tissue disease sera. The BMD assay was the most sensitive in detecting Scl-70. The immunoassays did not correlate well in the 57 SLE-defined sera; however, each had a variety of antibodies positive for each serum. The AtheNA assay demonstrated the highest degree of nonspecificity. Inova, BMD, AtheNA, and the Inova ANA HEp-2 IFA demonstrated 97%, 98%, 97%, and 99% specificity, respectively, using normal sera. Thus, all three assays showed a 97% or better negative predictive value. Positive correlation varied from 83% to 98%. Antibodies in SLE sera did not compare well among the three immunoassays. Significant variation in specificity and sensitivity due to individual characteristics of each assay was demonstrated, with the BMD assay showing the highest correlation with clinical diagnosis.