Anomalous pancreatico-biliary junction (APBJ) is commonly associated with cystic dilatation of the bile ducts but recently, several cases without the cystic dilatation have been reported. We treated a young female patient with intractable back and epigastric pain of three months duration. The spine was normal on magnetic resonance imaging (MRI), but several lymph nodes were seen around the coeliac axis. An APBJ, a non-cystic biliary system, non-filling of the gallbladder and an irregular right margin of the bile duct were evident on endoscopic retrograde pancreatography (ERCP), which was highly suggestive of gallbladder (GB) malignancy. At surgery, the GB was hard with local infiltration of the bile duct. Numerous large para-aortic and supraduodenal lymph nodes were present and only a biopsy was possible. Details of the case are presented and the growing etiological importance of an APBJ, especially without cystic biliary dilatation in gallbladder carcinogenesis is discussed.