The HLA-B27 antigen is an important genetic marker in ankylosing spondylitis (AS). Methods for the detection of B27 include the microlymphocytotoxicity test and, more recently, flowcytometry (FC). Here, we describe a new method, IMS-ELISA, for measuring the B27-antigen. It combines immunomagnetic separation (IMS), to obtain B27-positive cells from whole blood samples, with an enzyme-linked immunosorbent assay (ELISA) as a read-out. IMS-ELISA was tested on 367 samples obtained from five different hospitals in Taiwan. The sensitivity, specificity and accuracy of the method were compared with FC. Any conflicting data between IMS-ELISA and FC was confirmed by HLA-DNA typing via PCR-SSP (polymerase chain reaction-sequence specific primers). Overall, the results for sensitivity, specificity and accuracy obtained by IMS-ELISA and FC did not show any significant difference (p>0.05). However, when considering laboratory time, cost, ease of operation and the screening of large samples for HLA-B27, the IMS-ELISA was superior to the FC method. We conclude that IMS-ELISA may be used as a fast screening method for HLA B27 detection.