Abstract Background Anti-centromere antibodies (ACA), a type of anti-nuclear antibody (ANA) first identified as a discrete speckled pattern on indirect immunofluorescence assay (IFA), are a hallmark of systemic sclerosis (SSc), especially in its limited cutaneous form (lcSSc) or CREST (calcinosis, Raynaud’s, esophageal dysmotility, sclerodactyly and telangiectasia). These mitosis-related autoantibodies mainly recognize three centromere proteins (CENP), CENP-A, CENP-B, and CENP-C, that comprise the kinetochore important to chromosome segregation, but more recently, at least three other CENP antigens have been identified (CENP-D, CENP-E and CENP-F). Anti-CENP-B is considered the main autoantibody, and many, if not most, ELISA utilize recombinant CENP-B such that antibodies to CENP antigens other than CENP-B are not detected. Here, an ELISA using both CENP-B and CENP-A is compared to the reference method, HEp-2 cell IFA, highlighting its high, but still less than 100%, sensitivity due to multiple centromere subcomponents. Methods Anti-centromere antibodies are determined in patient serum using the reference method, IFA on the HEp-2 cell substrate (Sprinter XL/EUROpattern®, Euroimmun, NJ) which is also the current method for standalone ACA testing as well as screening by selected ANA profiles designed for the rheumatology specialist. Here ACA IFA- positive and negative serum samples were further analyzed by enzyme immunosorbent assay (ELISA) utilizing recombinant CENP-A and CENP-B (QuantaLyzer® 3000, Werfen, CA). Results When compared, samples between ACA pattern by HEp-2 cell IFA and anti- centromere antibodies by ELISA yielded an agreement of 93.2%. McNemar’s Test Chi Square of p>0.999, with a relative sensitivity of 89.7% and a specificity of 100.0%. Conclusions This study demonstrated very high concordance between ELISA and accurate ACA pattern identification on HEp-2 IFA. The ELISA studied here identifies autoantibodies to both CENP-A and CENP-B where many other ELISA identify only anti-CENP-B. Although ACA are relatively specific for SSc, they have also been reported in systemic lupus erythematosus (SLE), primary biliary cholangitis (PBC), rheumatoid arthritis (RA), Sjogren Syndrome, Raynaud's phenomenon and in cancer in individuals with or without evidence of systemic autoimmune rheumatic disease (SARD). Of note, many other commercially available ELISA for anti-centromere antibodies identify only anti-CENP-B, but there at least four other known CENP antigen targets for autoantibodies causing centromere pattern on IFA. Furthermore, almost all laboratories use the ELISA for ACA on ANA panel (or other connective tissue disease) screening. Hence, it should be duly noted that these testing strategies will not detect autoantibodies to all anti-centromere antibodies. Only specialized ANA profiles designed for the difficult-to-diagnose autoimmune patient begin screening using the IFA method for anti-centromere and therefore, are capable of detecting autoantibodies to all CENP antigens. Laboratorians should advise clinicians of these diagnostic limitations especially as our knowledge about centromere subcomponents and their clinical associations increases.