Objective To verify the diagnosis of the bacterial infections and to identify the pathogens, by PCR detection and bacterial endotoxin limulus test. Methods This study enrolled 50 patients receiving liver al-lografts from October 2005 to October 2007 in Ruijin Hospital. Peripheral blood samples were taken on DO, D1, D7 and D14. After preparation of the samples, PCR detection, bacterial endotoxin limulus test were performed. Results The sensitivity, specificity, and accuracy in the diagnosis was 66.7% ,95.0%, and 78.0% for the PCR, and 84.2%,83.9%,and 84.0% for limulus test respectively. It took 3 hours on average for the accomplishment of all these tests. Conclusions Positive PCR test plus negative limulus test suggest G+ infection, which may need the drugs targeting on G+ bacteria;positive PCR test plus positive limulus test, suggest G-infection or mixed infection, which may need drugs against the G-bacteria;negative PCR test, suggests the lack of severe infection. PCR test and limulus test were both remarkably faster than traditional cultural methods in diagnosis.