Cholangiocarcinoma (CCA) is a very heterogeneous group of neoplasms, for which the early diagnosis is difficult, present treatment methods are inadequate and the treatment effects are also limited. Thus, a detailed knowledge of the molecular pathological profiles of CCA is important for improving its diagnosis, treatment and outcomes. With the development of molecular biological technologies, the molecular pathological mechanisms of CCA will gradually be revealed and clarified, which may provide new ideas and approaches for early diagnosis and targeted therapy of CCA. Here, the authors present the current research progress in molecular pathology of CCA.