Bile stimulates many intestinal parasites, and newly excysted juvenile Clonorchis sinensis (CsNEJ) responds chemotactically to bile and matures in the bile duct. In this study, using annealing control primer-based polymerase chain reaction (PCR), 16 differentially expressed genes (DEGs) were found to be upregulated in C. sinensis metacercariae incubated in bile. Using contigs retrieved from a C. sinensis-expressed sequence tag pool, DEG sequences were extended further by DNA-walking. Of these, five DEGs were annotated to functional genes and confirmed to have been upregulated by more than twofold by quantitative real-time PCR. The gene products of these DEGs were cytochrome c oxidase subunit 2, phosphoenolpyruvate carboxykinase 2, and mitochondrial phosphate carrier protein, which are involved in energy generation, and HLA-B-associated transcript 3 and zinc finger protein, which are regulatory proteins associated with apoptosis and/or proliferation signaling pathways. Based on these results, it is suggested that bile stimulates the expressions of genes that produce the energy required by CsNEJs to migrate to the bile duct and to modulate the regulatory signals of cell proliferation associated with adult development.