Transcription factors (TFs) play a central role in regulating gene expression and in providing an interconnecting regulatory between related pathway elements. Currently, the wide-spread use of kidney transplantation to treat end-stage renal disease has evolved rapidly since the initial successful transplantations from both cadaveric and living donors. However, acute rejection is still a strong risk factor for chronic rejection in recipients of renal grafts. To investigate the possible mechanisms, we describe a comparison between TF' activity profile of acute rejection and controls. Through TF assay analysis and electrophoretic mobility shaft assay confirmation, we identified the activities of TFs in acute rejection after kidney transplantation. From a total of 345 screened TFs, 99 activity-differential TFs were found, of which 95 showed increased activity and four showed decreased activity. Our data indicate that TFs may be potentially involved in the pathogenesis of acute rejection, and can help to prevent, diagnose and treat acute rejection after kidney transplantation. The TF array methods could simplify the assay of multiple TFs and may facilitate high-throughout profiling of large numbers of TFs.