Background We have recently reported cytokine gene profile in kidney allograft recipients during the first week of transplantation. The mRNA transcripts of AIF-1 and IL-18 were enhanced in patient’s blood and particularly podocytes in kidney biopsy samples with rejection episodes. Our aim was to explore the significance of these markers in early kidney dysfunction vs. rejection episodes. We hypothesized that these markers may help to identify patients at high risk of developing DGF or allograft rejection after transplantation. Methods A total of 390 patients who received kidney transplant between 2007 and 2011 at University of Mississippi Medical Center were investigated. Clinical data were stratified, including DGF, stable graft function (SGF), and rejection episodes (RE), which were analyzed on the basis of cellular or antibody mediated rejection. The RE time points were: <6months; 6–12months; 13–36months, and >36months. Three blood samples from each patient at different time intervals were tested, using a q-RT-PCR and designated gene primers for inflammatory markers. Results In a global analysis, rejection episode rate was 16.92% (66/390). Separating the data on the basis of rejection time points we observed the following rates: 5.6% (22/66) for rejection episodes within <6months; 4.1% within 6–12months; 4.8% within 13–36months and 2.3% within >36months. The DGF was observed in 13.8%, SGF in 83% of patients after transplantation and 27 (7%) recipients returned to dialysis. IL-18 expression was significantly increased in patients who experienced DGF comparing the samples from pre-transplantation vs. day 3 and 6 post transplantation. AIF-1 was increased but not statistically significant. Both IL-18 and AIF-1 were significantly elevated during the first week of transplantation in patients who later experienced graft loss (p<0.001, and p<0.03 respectively). Conclusion The mRNA profiles of inflammatory markers observed in this study appeared to be predictive of allograft status and outcome. However, may not be useful to identify patients at high risk of delayed graft function.