The excisional surgical treatment of 50 patients with congenital biliary dilatation (CBD) associated with pancreaticobiliary maljunction (PBMJ) was analyzed. There were two patients who had early complications of lesser bile juice leakage with a maximum duration of 21 days, but no pancreatic juice leakage was noticed. As a late complication, two strictures at the anastomotic portion of the hepaticojejunostomy and one intrahepatic gallstone formation were encountered, but no malignant lesion was evident. Both patients with strictures could be predicted using postoperative cholangiography performed two weeks postoperatively and underwent hepaticojejunostomy. Intrahepatic gallstones were treated with lateral segmentectomy of the liver and electrohydraulic lithotripsy through percutaneous transhepatic cholangioscopy. Accordingly, these results suggest that excisional surgical treatment is the most appropriate method for CBD with PBMJ; however, special care must be taken, such as creating a sufficiently wide anastomotic stoma to enable free drainage of bile into the intestine; also, there should be precautions against ischemia at the anastomotic portion. The importance of the postoperative cholangiography to predict the postoperative outcome should be emphasized. Furthermore, causes of intrahepatic gallstone formation should be studied in such instances.