BACKGROUND The presence of intraduodenal peri-ampullary diverticulum is often observed during upper digestive tract barium meal studies and endoscopic retrograde cholangiopancreatography (ERCP). A few papers in China and overseas reported that the diverticulum had something to do with the incidence of cholelithiasis. This study was undertaken to further test this notion and ascertain the relationship between intraduodenal peri-ampullary diverticulum and biliary disease, especially the formation of bile duct pigment stones. METHODS A total of 178 patients who had undergone ERCP or endoscopic sphincterotomy (EST) were studied retrospectively. They were divided into 6 groups according to the category of biliary disease, and the incidence rates of intraduodenal peri-ampullary diverticulum were calculated. RESULTS There were 44 patients with intraduodenal peri-ampullary diverticulum in 81 patients with primary bile duct pigment stones (54.32%), 4 in 8 patients with bile duct stones and gallbladder stones (50%), 7 in 33 patients with bile duct stones secondary to gallbladder stones (21.21%), 3 in 21 patients with inflammation and stricture of the end of the bile duct and papilla (14.29%), 1 in 22 patients with carcinoma of the end of the bile duct and papilla (4.54%), and 5 in 13 patients with post-cholecystectomy syndrome or sphincter of Oddi dysfunction (38.46%). CONCLUSIONS The incidence rate of intraduodenal peri-ampullary diverticulum in patients with primary bile duct pigment stones is higher than that in patients with bile duct stones secondary to gallbladder stones, patients with inflammation and stricture of the end of the bile duct and papilla, and patients with carcinoma of the end of the bile duct and papilla. These findings indicate that the anatomical abnormalities and malfunction of the sphincter of Oddi play an important role in the formation of bile duct pigment stones.