Increased organ ischemia time leads to delayed graft function (DGF), increased acute rejection (AR), enhanced chronic allograft nephropathy (CAN) and reduced long term allograft survival. The mechanisms by which IRI predisposes to AR and CAN are unknown. We hypothesized that gene expression profiling of IRI-affected kidney would identify how IRI predisposes to AR and CAN. Furthermore, we examined how current immunosuppressive drug molecular targets are altered by IRI.C57BL/6J mice were exposed to 30 (n=3) or 60 (n=3) min of bilateral kidney ischemia or sham surgery (n=5). At 36 hr kidney tissue was collected and analyzed using Affymetrix 430MOEA (22626 genes) array and GC-RMA-SAM pipeline. Genes with the false discovery rate (q<1%) and ±50% fold change (FC) were considered affected by IRI. Genes coding for histocompatibility and antigen presenting factors, calcineurin and mTOR pathway-associated proteins were selected using Gene Ontology (GO) analysis. GO analysis identified 10 and 17 alloimmunity-related genes affected by IRI induced by 30 and 60 min of ischemia, respectively including Traf6 (FC=2.99) and H2-D1 (FC=2.58). We also detected significant IRI genomic responses in calcineurin and mTOR pathways represented by Fkbp5 (FC=4.18) and Fkbp1a (FC=2.0); Eif4ebp1 (FC=16.8) and Akt1 (FC=3.64), respectively.These data demonstrated that IRI upregulates expression of several alloimmunity-associated genes, which can in turn enhance alloimune responses. Our discovery of IRI-induced upregulation of genes associated with calcineurin and mTOR pathways are consistent with clinical observations that FK506 and Rapamycin can alter course of DGF. Further validation and dissection of these pathways can lead to novel approaches by which improved management of early "non-immune" transplant events can decrease susceptibility to more classic "immune" changes and CAN.