Pancreatic and biliary tract cancers are the most lethal malignancies in the gastrointestinal tract. Investigators have actively investigated to elucidate molecular mechanisms involved in the carcinogenesis, growth, invasion and metastasis of these cancers. This review describes those molecular mechanisms and their correlation with clinicopathological features of pancreatic and biliary tract cancers. Furthermore, recent experimental developments in the gene therapy technologies toward these cancers are also summarized.