Objective To comparatively study the ischemia-reperfusion injuries caused by heterogeneity of different positions of the biliary system and different construction patterns of the peribiliary vascular plexus. Methods Thirty rats were randomly divided into 3 groups: Group Ⅰ , sham operated; Group Ⅱ , 1h ischemia in biliary tract followed by 1h reperfusion; Group Ⅲ, 1h ischemia in biliary tract followed by 2h reperfusion. TUNEL assay, pathomorphology score determination and ultrastructural quantitative analysis were performed on epithelium of the hilar bile duct, proximal common bile duct and interlobular bile duct. Results In groupⅡ , TUNEL assay and pathomorphology score showed no statistical difference between proximal common bile duct and interlobular bile duct (P＞0.05) but showed significant differences in the hilar bile duct(P＜0.05). Mean volume (V) of mitochondria and area density of microvilli were obviously serious in the hilar bile duct but obviously slight in the proximal common bile duct(P＜0. 05). In group Ⅲ, the results of the above detections showed that the most severe was in hilar bile duct, followed by the interlobular bile duct and proximal common bile duct(P＜0. 05). Conclusion Different injuries in various parts of the biliary system are caused by heterogeneity of biliary epithelial cells and construction patterns of the peribiliary vascular plexus. It also provides the experimental basis to explain the higher incidences of hilar bile duct stricture. It could be taken as the best position when the bile duct is anastomosed.