Aim The purpose of this study was to evaluate the effectiveness of our laboratory’s use of pronase-treated lymphocytes in reducing the detection of non-specific binding (autoreactivity/autoantibodies) in the flow cytometry crossmatch. Method 22,841 flow cytometry crossmatches performed in our laboratory between 1998 and 2014 were evaluated for the frequency of detection of autoantibodies. Crossmatches were performed either with non-treated lymphocytes (n = 10,275, years 1998–2006) or with pronase-treated lymphocytes (n = 12,566, years 2006–2014). All crossmatches included an autologous control (patient’s serum tested against patient’s cells). Results Percentage of crossmatches exhibiting autoreactivity. Cell treatment Autoreactivity with either T-cells or B-cells Autoreactivity with T-cells and B-cells Autoreactivity with T-cells only Autoreactivity with B-cells only No pronase treatment (n = 10,275) 16.8% (1727) 6.7% (685) 1.3% (129) 8.9% (913) Pronase treated (n = 12,566) 6.2% (785) 1.2% (148) 1.0% (125) 4.1% (512) Conclusion Pronase-treatment of lymphocyte targets in the flow cytometry crossmatch greatly reduces the percentage of flow cytometry crossmatches whose interpretation is compromised by the detection of autoreactivity. The percentage of crossmatches that exhibited autoreactivity fell from 16.8% when pronase was not used, to 6.2% when lymphocytes were treated with pronase.