BACKGROUND: Microbial infections and translocation of intestinal bacteria are thought to contribute to multiple system organ failure, but bacterial cultures are often negative in patients with this complication. The purpose of this study was to determine the sensitivity of PCR for detecting microbial DNA in the blood of animals after conducting an experimental model of anastomotic leakage. METHODS: Fourty rats were divided into three groups as follows: Control Group; simple laparotomy group, Anastomosis Group; colon resection and anastomosis group, and Leakage Group; group with colon resection and an anastomosis leaving a 5 mm opening. Blood was drawn form rats before the procedure, and postoperative 3rd and 6th days. DNAs were extracted from these samples and PCR techniques were used to amplify genes of Escherichia coli. Statistical analysis for the percentage of rats with microbial DNA in the blood for all groups was done by Fishers exact chi- square test. The difference among groups was considered significant if the P value was less than 0.05. RESULTS: Most of the detected Escherichia coli genes were from the Leakage Group, and the detection rate was significant compared to other groups. CONCLUSION: We suggest that PCR could be a useful adjunct tool for immediate diagnosis of anastomotic leakages.