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Deceased-donor (DD) kidneys are at higher risk for ischemia/reperfusion injury leading to increased inflammatory mediators and innate immune response. We aimed to investigate the effects of prolonged cold ischemia on intragraft molecular gene expression profiles of DD kidneys comparing to living-donors (LD) pre-implantation biopsies using microarrays.There were 48 pre-implantation kidney biopsy samples (29 LD and 19 DD). The cold ischemia time (CIT) was < 16 hours in 10 and > 16 hours in 9 DD kidneys. The gene expression profiles were studied by Affymetrix HuGene 1.0 ST expression arrays.There were 198 differentially expressed genes when pre-implantation DD biopsies were compared to LD biopsies (Both False discovery rate p<0.05 and fold change >2). Pathogenesis based transcripts (PBT) showed increased transcripts associated with injury and response (IRIT), Constitutive Macrophage (CMAT), and Gamma Interferon (GRIT) in DD samples compared to pre-implantation LD biopsies. There was no difference in Cytotoxic T-cell (CAT), Natural-Killer cell (NKAT), B-cell (BAT), and Endothelial cell (ENDAT) associated gene transcripts between 2 groups. However, there was no statistically significant difference in expression of any PBTs studied when biopsies with CIT > 16 hours compared to biopsies with CIT < 16 hours. Gene Ontology analysis showed that DD preimplantation biopsies had increased expression of pathways related to acute inflammatory response, lymphocyte mediated immunity, innate and humoral immune response, complement activation and regulation of immune response and IL-6 activation.Pre-implantation DD kidney biopsies showed increased expression of gene transcripts associated with inflammatory mediators, cytokines, macrophages, innate immune response and response to injury compared to LD kidneys. However, increased cold ischemia time does not change the intragraft gene expression profiles.