Biliary pancreatic duodenal junction is a special region in the human body. It is difficult to diagnose and treat diseases in this region because of the complicated anatomy, the limitation of diagnosing methods, the variety of disease, the high risks of operation and the severity of complications. We should pay more attention to the pathophysiology aspects and the laboratory researches of diseases in this region. Proper diagnosis and combination of different diagnosing methods could improve the rate of early diagnosis and identify the characteristics of the disease. Individualized operation should be considered to deal with iatrogenic injury of biliary pancreatic duodenal junction according to different patients′ condition. The principle of operation is to control damage firstly and to preserve the function of biliary pancreatic duodenal junction and the physiological passway of bile and pancreatic juice to the greatest extent.