We conducted a comprehensive comparison in the sensitivity, specificity, dilution sensitivity, and precision between two immunoassay systems, Roche Elecsys Cobas e 601 and Sysmex HISCL 5000, for the detection of hepatitis B virus surface antigen (HBsAg), antibody to hepatitis C virus (anti-HCV), treponemal antibodies (anti-TP), and human immunodeficiency virus (HIV). One thousand unselected samples and 100 reserved weak reactive samples were tested by the two systems. Sensitivity and specificity were then calculated for each system. Seroconversion panels were used to assess the sensitivity in early stage detection. Dilution sensitivity was evaluated by dilution tests of several seroconversion panel samples. Evaluation of within-run and intermediate precision was conducted following EP-15A protocol. The consistency rates of the two systems for the detection of four pathogens were all over 99% among unselected samples. Both Elecsys and HISCL were observed to have high sensitivity and specificity in unselected samples and weak reactive samples. Seroconversion panel tests showed that Elecsys could identify positive results earlier than HISCL in HBsAg (1 out of 4), anti-TP (1 out of 2) and HIV (1 out of 12) panels. The results of the anti-HCV panels were comparable. In dilution tests, Elecsys could detect lower concentrations than HISCL in two anti-HCV samples and one anti-TP sample. The two systems had similar performance in dilution tests of HBsAg and HIV samples. Both Elecsys and HISCL had qualified intra-assay and inter-assay precision. Both Elecsys and HISCL have good performance in the screening of four common bloodborne pathogens. The two systems are comparable and considered adequate for clinical use.