The effects of polychlorinated biphenyls (PCBs) on liver function and their differences between sexes were analyzed in Japanese medaka (Oryzias latipes) exposed to PCB126 or Kanechlor-400 (KC-400) using microarray. PCB exposure induced vitellogenin 1 expression in female medaka while suppressing choriogenin genes, which suggests that the effects of PCBs on estrogen-responsive genes do not occur directly through an estrogen receptor-mediated pathway. Reduction of androgen receptor alpha expression was also observed, and the gene expression pattern in PCB-exposed males changed to become more similar to that of females. Furthermore, changes in glycolysis-related genes indicate that PCB exposure might enhance glucose production via gluconeogenesis in the liver of medaka. Taken together, our results suggest that PCBs disrupt the endocrine system, especially androgen function, and may have the potential to cause demasculinizing effects. Additionally, induction of gluconeogenesis might be a response to maintain glucose levels consumed as a result of PCB exposures. © 2011 Elsevier Ltd.