Objective: To investigate the effects of different biliary drainage methods on the intestinal mucosal barrier function in rats with obstructive jaundice (OJ) and the mechanisms. Methods: Sixty SD rats were used to establish OJ models by common bile duct ligation. One week after operation, the rats were equally randomized into non-drainage group (underwent no biliary drainage), internal drainage group (underwent internal biliary drainage) and external drainage group (underwent external biliary drainage), and the drainage time was one week. Twenty SD undergoing sham operation served as control group and the total experiment time was two weeks. At the end of the experiment, the serum endotoxin level and protein expression of occludin and zona occludens 1 (ZO-1) in the tissues of small intestinal mucosa of each group were determined by ELISA assay and Western blot analysis respectively, and the histomorphological changes in small intestinal mucosa were also observed. Results: Rats presented overt symptoms after OJ model creation, while the general conditions of rats of internal drainage group were better than those of non-drainage group and external group after the second operation. The serum endotoxin levels in OJ rats of non-drainage group and external drainage group were increased markedly, and their differences versus control group reached statistical significance (both P<0.01), but no significant difference was observed between the two drainage groups (P>0.05); the serum endotoxin level in OJ rats of internal drainage group was significantly lower than that in OJ rats of non-drainage group or external drainage group (both P<0.01), and showed no significant difference versus control group (P>0.05). Compared with control group, the protein expressions of occludin and ZO-1 in small intestinal mucosa in rats of non-drainage group and external drainage group were significantly decreased (all P<0.01), and the degree of decrease in external group was more evident than that in non-drainage group (both P<0.01); the expression levels of the two proteins in internal drainage group were significantly higher than those in non-drainage group or external drainage group (all P<0.01), and were similar to those in control group (both P>0.05). As seen at the pathological examination, the intestinal mucosal integrity was damaged in OJ rats of both non-drainage group and external group with large or moderate amounts of inflammatory cell infiltration, while the intestinal mucosal integrity was maintained intact with less inflammation in OJ rats of internal drainage group. Conclusion: Internal biliary drainage has protective effect on the intestinal mucosal barrier in OJ rats, and the mechanism is probably due to the maintaining effect of bile on tight junction-related protein expression in intestinal epithelial cells.