Renal ischemia-reperfusion injury (IRI) is an invariable consequence of transplantation. The tubuloepithelial expression of CD44 is markedly enhanced in autoimmune renal injuries. The aim of this experimental study was to evaluate the effect of IRI on the expression of CD44 in rat kidney. Thirty male Sprague-Dawley rats were used. The rats were divided into three groups. The rats in group 1 (n = 10) underwent laparotomy and left nephrectomy (Sham surgery). The rats in group 2 (n = 10) underwent laparotomy, 1 h renal ischemia, followed by 1 h of reperfusion and then left nephrectomy was performed. The rats in group 3 (n = 10) underwent laparotomy, 1 h renal ischemia, followed by 24 h of reperfusion and then left nephrectomy was performed. Histopathological findings and the immunohistochemical expression of CD44 in ischemic and reperfused rat kidneys were investigated. In histopathologic evaluation, non-specific changes were observed in group 2 and early phase of IRI were present in group 3. CD44 was expressed in both group 2 and 3 but not in group 1. The mean immunohistochemical staining percentages of rat kidneys in group 1, 2, and 3 were 0.00 +/- 0.00, 39.90 +/- 5.53, and 26.20 +/- 8.38, respectively. The immunohistochemical staining pattern was more dense in group 2 than in group 3 (P < 0.001). In conclusion, the expression of CD44 in renal tubuloepithelial cells was significantly increased after IRI. The increase in CD44 expression was more prominent during the early phase of IRI and started to decline after 24 h of reperfusion.