Background: C57BL/6 and 129/Sv are the 2 most commonly used strains of mice in renal ischemia-reperfusion injury (IRI) studies, yet there are currently no studies that contrast differences in the degree of renal injury after ischemia-reperfusion. Methods: To evaluate renal IRI in male C57BL/6 and 129/Sv mice, we performed unilateral clamping of the left renal pedicle for 45 minutes and compared the degree of renal tissue damage and function. To measure function and tissue damage we examined: glomerular filtration rate (GFR; by inulin clearance), renal blood flow (RBF; by p-aminohippurate [PAH] clearance), renal morphology, immunohistochemistry for infiltrating leukocytes, and fibrogenic markers by Sirius red staining. Results: After unilateral IRI, 129/sv mice had significantly less GFR and RBF disfunction at both day 14 (d14) and d28. 129/sv mice also had significantly less acute tubular necrosis on d1 and fewer infiltrating leukocytes on d28, as well as less collagen deposition on d28 than C57BL/6 mice. Conclusions: C57BL/6 mice were much more sensitive to damage caused by renal IRI than are 129/Sv mice.