We analyzed clinical features and genetic alterations in the noncancerous and cancerous biliary lesions obtained from pancreaticobiliary maljunction (PBM) patients. Gallbladder (GB) and bile duct (BD) lesions were obtained surgically from 36 patients with PBM, and polymerase chain reaction (PCR) methods were used to examine for mutations of the K-ras gene and the p53 gene and for microsatellite instability (MSI). The 36 cases were clinically classified into two types according to whether extrahepatic bile duct dilatation was present: a congenital choledochal dilatation (CCD) group (n = 20) and a noncongenital choledochal dilatation (NCCD) group (n = 16). In the NCCD group, all 16 GB specimens exhibited hyperplastic, dysplastic, and cancerous (n = 9) lesions, but no pathological lesions were detected in the 12 BD specimens. On the other hand, in the CCD group, pathological examination revealed lesions, including 8 cancerous lesions, in 60% of the 20 GB specimens and lesions, and including 8 cancerous lesions, in 65% of the 20 BD specimens. K-ras mutations and MSI were detected in 33.3% and 0%, respectively, of 9 hyperplastic lesions, 28.6% and 85.7%, respectively, of 7 dysplastic lesions, and 60.0% and 80.0%, respectively, of 25 cancerous lesions (p <0.05; MSI in hyperplasia vs. dysplasia and cancer). There was no difference of the frequency in K-ras mutations and MSI between the NCCD and CCD groups. By contrast, p53 mutations were detected only in the cancerous GB lesions of both types, the rate being 35.3%. Genetic alterations of K-ras, MSI, and p53 are strongly associated with biliary tract cancer in PBM patients. MSI appears to contribute to carcinogenesis in the biliary tract mucosa of PBM patients, and p53 mutations may be related to the development of GB cancer in the CCD group.