Abstract: Methods are disclosed for, early diagnosing chronic rejection (CR) in a transplanted subject, monitoring CR in a transplanted subject at risk of developing CR, preventing, inhibiting, reducing or treating CR in a transplanted subject, or identifying agents for use in the prevention, inhibition, reduction or treatment of CR, based on genes which are differentially expressed in transplant biopsy tissues, before any overt clinical or histological manifestation of CR is detected in the transplanted subject.