The purpose of this study was to evaluate the intestinal microflora and the composition of various bile acids in jejunal fluid following B-I and B-II types of biliary reconstruction in dogs. B-1 type reconstruction, in which the biliary tract was directly anastomosed to the food passing tract, was performed in 8 dogs, which received cholecystoduodenostomy (group C-D) and in 8 which received cholecystojejunostomy (group C-J). B-II type reconstruction by Roux-Y cholecystojejunostomy, in which bile flowed into the jejunal limb, was performed in 8 dogs (group R-Y). Incidences of detection of gram-positive, gram-negative and anaerobic bacteria were as follows: 33%, 33% and 6% in the jejunal fluid obtained at initial operation, 67%, 67% and 33% in group C-D, 83%, 67% and 33% in group C-J, and 75%, 88% and 75% in group R-Y. In six dogs in group R-Y, unconjugated or secondary bile acids in the jejunal fluid increased, while these increases were observed in only two dogs in group C-J and in no dogs in C-D. Unconjugated and secondary bile acids were more likely to increase following B-II type reconstruction than following B-I type reconstruction. These findings are thought to be associated with bacterial overgrowth in the jejunal loop. These results suggest that B-II type reconstruction, in which bilio-enterostomy is exposed with infected intestinal fluid and unconjugated and secondary bile acids, is inferior in preventing ascending cholangitis.