The molecular mechanisms underlying the development, growth and metastatic diffusion of biliary tract cancers are still undefined. The increase in worldwide incidence and mortality of cholangiocarcinoma justifies the impellent need to clarify the intracellular mechanisms triggering the malignant transformation of the biliary epithelium and growth of biliary malignancies. A more complete characterization of the molecular pathology of bile duct cancers could lead to the identification of valid targets for the diagnosis and therapy of these devastating malignancies. This review describes the scientific progress made over the past decades with regard to the understanding of the molecular processes of cholangiocarcinogenesis.