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Background: Flow cytometry crossmatch (FCXM) is the most sensitive method currently used for human leukocyte antigen (HLA) crossmatches. The FCXM test methods and cut-off values used to determine the positive reaction vary significantly in different laboratories. To obtain comparable FCXM results from different laboratories and to use these results in deciding the compatibility between a donor and a recipient in organ transplantation, a standardized protocol needs to be established. In this study, we attempted to develop a harmonized test method and verify its performance with that of the different laboratories’ methods through a multicenter comparison. Methods: The harmonized method was determined via a literature review and a survey that included seven laboratories. For the harmonized method, cell number, serum amount, pronase treatment for B cell FCXM, incubation temperature and time, and anti-human immunoglobulin G fluorescein isothiocyanate conjugate were standardized. Two trials of FCXM using one cell and three sera samples in each trial were performed, and the results of the laboratories’ methods versus those of the harmonized method were analyzed. Results: Compared to the laboratory methods, the harmonized method showed increased agreement with consensus positive/negative results (75/84, 89.3% vs. 81/84, 96.4%) and a significantly decreased coefficient of variation among different laboratories in detecting the median fluorescence intensity (MFI) ratio values (88.3% vs. 55.2%, P =0.0003). Conclusions: When the same protocol for the FCXM method is used, an increased consensus of positive/negative results and decreased variation of the MFI ratios from different laboratories can be obtained. Implementation of a harmonized and standardized protocol is needed in all domestic laboratories that perform the FCXM tests.