This study aimed to compare the effect on renal functions of ischemia-reperfusion (I-R) injury models by renal scintigraphy and to investigate possible correlations among scintigraphic, biochemical and pathological findings. An experimental I-R injury was performed on the left kidneys of 40 Wistar rats: pedincular continuous clamping in Group 1 (n = 10), pedincular cyclic clamping in Group 2 (n = 10), arterial continuous clamping in Group 3 (n = 10) and arterial cyclic clamping in Group 4 (n = 10). A functional and morphological assessment was made by (99m)Tc-MAG3 scintigraphy, biochemical tests and histopathological examination in the late period of I-R injury. Data were analyzed statistically. Statistically significant differences were found in the peak counting (C max), normalized residual activity (NORA), renal retention (RR), split renal function (SRF) and the time to the C max (T max) parameters between the right and left kidneys in each group (p < 0.001). In multiple group comparisons for the left kidney statistically significant differences were determined for C max (F = 4.75, df = 3, p < 0.05), NORA (F = 4.362, df = 3, p < 0.05), RR (F = 10.49, df = 3, p < 0.001) and SRF (F = 4.17, df = 3, p < 0.05) but not T max (F = 1.13, df = 3, p > 0.05). The total scores of Groups 1, 2, 3, and 4 were, respectively, found to be 18, 30, 20 and 24 by grading of renogram curves and 22, 28, 23 and 25 by pathological scoring system. There was a significant correlation among the two score data (r = 0.867, p < 0.001). (99m)Tc-MAG3 scintigraphy was a reliable method to evaluate renal dysfunction in the late period of I-R injury. Cyclic clamping, especially pedincular type was compatible with higher tubular dysfunction and structural damage.