A patient with chronic pancreatitis caused by congenital pancreatic duct atresia underwent total pancreatectomy and mixed-cell pancreatic autotransplantation by portal vein embolization. Two years later she developed massive upper gastrointestinal bleeding from gastroesophageal varices and required a mesocaval H graft. The cause of the portal hypertension was portal vein thrombosis caused by portal vein infusion of pancreatic homogenate, and it represents a serious complication of the procedure. Although this is the second report of portal hypertension that required portasystemic shunting after islet cell autotransplantation, it is the first reported case of the development of bleeding esophageal varices caused by portal vein thrombosis after pancreatic islet cell transplantation.