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Severe injuries of biliary or pancreatic ducts are associated with significant morbidity and mortality. Severe bile duct injuries such as major biliary leaks, complete transection, or complete occlusion of bile ducts can be grouped under the term complex bile duct injuries (CBDI). In the spectrum of pancreatic duct injuries, disconnected pancreatic duct syndrome (DPDS) represents the most severe form and most often occurs after a severe episode of acute pancreatitis. Treatment of these complex injuries is quite challenging and for many years surgical management has been considered the treatment of choice. However, in the past few years, some studies have reported the successful management of CBDI or DPDS using endoscopic procedures alone or in combination with a percutaneous approach. In this review, we detail the endoscopic or combined endoscopic/percutaneous treatment possibilities for CBDI and DPDS.