PURPOSE: A high yield of viable pancreatic islets is an essential prerequisite for the study of pancreatic islet transplantation. The purpose of this study is to compare the yield between intra-gall bladder (intra-GB) and intra-common bile duct (intra-CBD) injection of collagenase solution for isolation of mouse pancreatic islets. METHODS: The mice were divided into two groups, the intra-GB and intra-CBD groups, and each group included twelve mice, respectively. Collagenase solution was injected via the gallbladder in the intra-GB group mice, while this was done via the common bile duct in the intra-CBD group. After removal and digestion of the mouse pancreases, the pancreatic islets were isolated by Ficoll density gradient centrifugation and hand picking. RESULTS: The intra-GB group yielded 121.67+/-39.86 IEQs, and the intra-CBD group reveled 168.17+/-29.23 IEQs. There was a statistically significant difference in islet yield between the two groups (P=0.005, Mann-Whitney Test). The purities of the isolated islets were 86.42+/-3.99% for the intra-GB group and 87.17+/-4.47% for the intra-CBD group, and there was no difference between the two groups (P=0.755, Mann- Whitney Test). CONCLUSION: Both the intra-GB and intra-CBD groups yielded an average of >120 IEQs. However, the intra-CBD group revealed a higher yield than the intra-GB group for isolating mouse pancreatic islets.