The present invention relates to a composition for preventing or treating chronic allograft dysfunction, comprising bisphosphonate which is used as a therapeutic agent for osteoporosis. The composition for preventing or treating chronic allograft dysfunction, comprising bisphosphonate, according to the present invention has an excellent prophylactic and/or therapeutic effect on chronic allograft dysfunction caused by a gradual decrease in the function of a transplanted tissue or organ which occurs after tissue or organ transplantation surgery, and thus is expected to be able to remarkably increase a long-term survival after transplantation surgery.