Ischemia reperfusion (I/R) injury plays a major role in delayed graft function and long-term changes after kidney transplantation. By using different therapeutic strategies to prevent I/R injury in rat models of kidney transplantation we studied relationships between inflammatory cell arrival and adhesion molecule expression. In other rat models for acute renal failure we investigated the effect of up-regulation of protective genes such as heme oxygenase-1 (HO-1) on infiltrating cells, showing that infiltrating cells also contribute to beneficial effects. In order to gain more insight into the complex mechanisms of long-term changes after kidney transplantation, we started a protocol biopsy program to study histologic changes 6, 12, and 26 weeks after transplantation. The following article clarifies some of the complex mechanisms contributing to long-term changes caused by I/R injury.