BACKGROUND AND AIMS: Recently, similar to the anomalous union of the pancreatobiliary duct (AUPBD), a low junction of the cystic duct (LJCD) was reported to be associated with the carcinogenesis of the gall bladder (GB) and other pancreatobiliary diseases. This study was designed to evaluate the clinical significance of the LJCD. METHODS: In this study all cases were performed ERCP. Three hundred and twenty two cases were selected due to their clear identification of the union area between the bile duct and the pancreatic duct, inserted area of the cystic duct, and the duodenal opening of the bile duct. The LJCD was defined that the cystic duct joins the distal bile duct between the upper margin of the pancreas and the duodenal opening of the bile duct. AUPBD was defined as a common channel greater than 15 mm in length. The clinical data was divided into four groups-normal biliary anatomy (Group 1), AUPBD (Group 2), LJCD (Group 3), and combined with AUPBD and LJCD (Group 4), and then analyzed. RESULTS: The mean age of the subjects was 56.6 with 183 male and 139 female cases. Among 322 cases, there were 7.1% (23 of 322) of AUPBD, 11.2% (36 of 322) of LJCD and 0.6% (2 of 322) of combined with AUPBD and LJCD. The clinical symptoms and the laboratory findings of the subjects were no statistical significance among the groups. The incidence of CBD stones was 27.3% (88 of 322) of the patients; 25.3% (66 of 261) of Group 1, 21.7% (5 of 23) of Group 2, 47.2% (17 of 36) of Group 3, and were significantly higher in Group 3 than Group 1 & Group 3 (p=0.038). However, the incidence of GB stones and cystic duct stones was no statistical significance among the groups. Malignant diseases of the biliary trees were 9.65% (31 of 322) of the patients; 6.8% (18 of 261) of Group 1, 26% (6 of 23) of Group 2, 13.8% (5 of 36) of Group 3, and were closely correlated with AUPBD (p<0.001) and LJCD (p=0.017). CONCLUSIONS: LJCD is relatively common in patients undergoing ERCP and closely correlated with the CBD stones and the malignacies of the biliary system. However its role in these condition is uncertain and needs to be further investigated.