BACKGROUND: Flow cytometric crossmatching (FCXM) is widely used in hospitals performing solid organ transplantation. Pronase treatment of lymphocytes can increase the sensitivity and specificity of B-cell FCXM. However, it can also affect human leukocyte antigen (HLA) expression and results of FCXM. We treated lymphocytes with various concentrations of pronase and analysed the effect of the treatment on the FCXM results. METHODS: The peripheral blood mononuclear cells isolated from 10 renal transplant donors were treated with three different concentrations of pronase (0.5, 1.0, and 2.0 mg/mL). The effects of pronase on median fluorescence intensity (MFI) values of AB serum (Fcγ receptor), HLA class I and II, and on the MFI ratio of HLA class I and II were analysed. RESULTS: In B-cell FCXM, the MFI values of AB serum (Fcγ receptor) and HLA class I were significantly decreased by the pronase treatment. The MFI ratio of HLA class II was significantly increased upon treatment with 0.5, 1.0, and 2.0 mg/mL pronase (P<0.05, P<0.01, and P<0.01, respectively). In T-cell FCXM, the MFI ratio of HLA class I was significantly decreased by the pronase treatment (all P<0.01). CONCLUSIONS: When performing FCXM, it is recommended that B-lymphocytes should be treated with 1.0 or 2.0 mg/mL pronase. In the case of T-lymphocytes, pronase treatment should be adopted with caution.