Cholangiocarcinomas are neoplasms that involve the epithelial cells of the bile duct, also known as cholangiocytes. This disease is difficult to diagnose early, as most symptoms present late in the disease. In addition, the specific anatomic position can cause periductal extension and result in a very low radical excision rate and a very poor prognosis. Improved understanding of the features underlying the onset of cholangiocarcinoma and its carcinogenic mechanism may lead to early diagnosis and better prognosis. With the development of molecular biology, much has been learned about oncogenes, tumor-suppressor genes, DNA methylation, microRNAs, and the molecular mechanisms of tumor invasion and metastasis. Based on our research and others, this review article will discuss the current status and prospects of early diagnosis of cholangiocarcinoma.