Objective To observe the influence of connexin 43 (Cx43) on bystander effects induced by cytosine deaminase (CD) and herpes simplex virus thymidine kinase (HSV-tk) coexpression suicide genes system in human cholangiocarcinoma QBC939 cells and transplantation tumors in nude mice. Methods In vitro, the CD+tk+ and CD+tk+Cx+ cells were respectively treated with 5-fluorocytosine (5-FC) and ganciclovir (GCV). The cytotoxic efficacy was evaluated by microculture tetrajolium test (MTT) method. In order to investigate the influence of Cx43 on bystander effects, the volumes of transplantation tumors of the CD+tk+ and CD+tk+Cx+ cells were measured before and after application of 5-FC and GCV. Results CD and tk gene were stably expressed in transfected QBC939 cells. Increasing expression of Cx43 was determined by testing for the presence of Cx43 mRNA by RT-PCR and the presence of Cx43 protein by Western blot in CD+tk+Cx+ cells. The killing effect of 5-FC and GCV on CD+tk+Cx+ cells was more effective than that on CD+tk+ cells both in vitro and in vivo. Conclusion Double suicide genes system CD/5-FC+tk/GCV could induce remarkable killing effect on cholangiocarcinoma cells in vitro and transplantation tumors in vivo. The cotransfection of Cx43 gene is able to enhance the bystander effects and the inhibition of carcinoma cells.