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Background Techniques for the fast and accurate detection of bacterial infection are critical for early diagnosis, prevention and treatment of bacterial translocation in clinical severe acute pancreatitis (SAP). In this study, the availability of a real-time PCR method in detection of bacterial colonization in SAP rat models was investigated.Methods Samples of blood, mesenteric lymph nodes (MLN), pancreas and liver from 24 specific pathogen-free rats (8 in a control group, 16 in a SAP group) were detected for bacterial infection rates both by agar plate culture and a real-time PCR method, and the results were made contrast.Results Bacterial infection rates of the blood, MLN, pancreas and liver in the SAP group and the control group by the two different methods were almost the same, which were 5/16, 12/16, 15/16, 12/16 in the SAP group compared with 0/8, 1/8, 0/8, 0/8 in the control group by agar plate culture, while 5/16, 10/16, 13/16, 12/16 and 0/8, 1/8, 0/8, 0/8 respectively by a real-time PCR method. Bacterial number was estimated by real-time PCR, which showed that in the same mass of tissues, the pancreas contained more bacteria than the other three kinds of organs in SAP rats (P <0.01), that may be due to the edema, necrosis and hemorrhage existing in the pancreas, making it easier for bacteria to invade and breed.Conclusion Fast and accurate detection of bacterial translocation in SAP rat models could be carried out by a real-time PCR procedure.