Background: Due to the increasing need for kidney donors, transplantation from non-heart-beating donors (NHBD) is currently being practiced more extensively. As detailed studies on the reperfusion injury of these kidneys do not exist so far, a comparison of renal ischemia reperfusion injury scores immediately after organ explantation with injury scores after NHBD organ explantation with subsequent cold storage would be useful. Methods: Non-stored kidneys were compared to a group of kidneys stored for 6.9 ± 1.8 h. Functional analyses were made during 145 min of ex vivo perfusion. Quantitative histological analyses were performed in all kidneys after termination of perfusion. Results: During ex vivo reperfusion, renal vascular resistance was elevated, while creatinine clearance, filtration fraction, renal oxygen consumption, and sodium reabsorption were below normal after non-heart-beating explantation and further decreased after subsequent washing and cold storage. In the kidneys subjected to cold preservation, histologically tubular damage was enhanced, and the total count, as well that for the intraglomerular neutrophil granulocytes were also elevated. Conclusions: Explantation from NHBD causes renal ischemia reperfusion injury. Cold storage augmented deterioration of the kidney as histologically and functionally demonstrated. Thus, preservation times for non-heart-beating kidneys should be carefully reappraised.