BACKGROUND: HLA-B27 typing has long been performed by the microlymphocytotoxicity method(MCT) but the flow cytometry method(FCM) was introduced several years ago. False positive results due to the HLA-B7 cross reactive groups(CREG) were the main drawback of the serologic method. The authors performed polymerase chain reaction-sequence specific primer(PCR-SSP) test for HLA-B27 to compare the results with serologic methods. METHODS: PCR-SSP test for HLA-B27 was performed on four hundred forty one samples. Three hundred twenty eight samples were tested by MCT and one hundred thirteen samples by FCM. PCR-SSP for HLA-B27 subtyping or Amplification Refractory Mutation System-PCR(ARMS-PCR) for HLA-B typing was performed on twenty four discrepant samples. RESULTS: The concordance rate between MCT and PCR-SSP was 92.9%(305/328) and the concordance rate between FCM and PCR-SSP was 99.1%(112/113). Twenty four(5.4%) out of four hundred forty one samples showed discrepancy between serologic methods and PCR-SSP method. Fourteen out of one hundred MCT positive samples and only one out of forty FCM positive samples showed negative by PCR-SSP. Nine samples showed PCR-SSP positive and MCT negative. CONCLUSIONS: The false positive rate of MCT was quite high and there were some false positive and negative results by PCR-SSP, too. From the above findings, we suggest that FCM is the most accurate method for HLA-B27 typing in those laboratory equipped with flow cytometry.