Abstract: OBJECTIVE To evaluate the clinical application value of polymerase chain reaction (PCR) in the diagnosis of spontaneous bacterial peritonitis (SBP) in patients with liver cirrhosis through the detection of 16S rRNA. METHODS A total of 77 patients with liver cirrhosis in decompensated period combined ascites in our hospital from Dec. 2014 to Oct. 2015 were selected. Using bacterial 16S rRNA gene as the target sequence, specific sequences were selected to establish a rapid diagnostic method in the universal and specific region. The bacterial DNA in ascites of the patients with liver cirrhosis was detected by this method, and the results were compared with the conventional methods. SPSS 16.0 was used for data analysis. RESULTS From the 77 submitted specimens, 50 cases (64.9%) were positively amplified by 16S rRNA universal sequence and 15 cases (19.5%) by specific sequence through PCR method. Taking ascites culture positive, PMN≥250×10⁶/L or (and) peritoneal irritation sign positive and anti-infection treatment effective as SBP diagnostic gold standard, in which the sensitivity of PCR method was 100.0%, the specificity 54.0%, the positive predictive value 54.0%, the negative predictive value 100.0%, and the difference between the two groups was significant (χ²=22.453,P<0.01). CONCLUSION Compared with the traditional methods, the PCR assay is a more sensitive and simple method which is a certain value of the detection of ascites in patients with liver cirrhosis.