Clonorchiasis is associated with bile duct malignancy and the subsequent development of cholangiocarcinoma. Although this is likely caused by adult Clonorchis sinensis and its excretory-secretory products (ESP), the precise molecular mechanisms remain obscure. To evaluate the effect of C. sinensis infection on differential gene expression in host hepatocytes, we examined the kinetics of changes in gene expression in the human cholangiocarcinoma cell line HuCCT1 treated with ESP at different times. Using complementary DNA microarrays containing 23,920 human genes of known function, we initially identified 435 genes altered by ESP treatment. Of these, 31 were up-regulated and 35 were down-regulated more than twofold in a time-dependent manner following ESP treatment. Clustering of these genes by function revealed that several were involved in the cell cycle, oncogenesis, protein modification, immunity, signal transduction, cell structure, and developmental processes. These findings should provide a fundamental basis for further analysis of the molecular pathways and mechanisms involved in C. sinensis infection of host cells.