Background We compared the effect of temporary aneurysm clips on atherosclerotic and nonatherosclerotic CCA of rabbits by morphometric and ultrastructural methods. Materials and Methods The rabbits (N = 12) were divided into 2 groups: the first group was fed a 2% cholesterol diet, and the second group, a normal diet for 4 weeks. Atherosclerotic lesions developed after 4 weeks. Temporary aneurysm clips were placed on the left CCA of both groups; the right CCA of both groups served as control. Thus, a total of 4 groups were used: atherosclerotic (A), atherosclerotic/clip (AC), nonatherosclerotic (NA), and nonatherosclerotic/clip (NAC). Temporary aneurysm clips were applied for 1, 5, and 10 minutes in the AC and NAC groups. No temporary clip was placed on the right CCA (A and NA groups). The affected parts of the CCA via clips were examined under light microscope and SEM. Results Comparison of atherosclerotic and nonatherosclerotic CCA of rabbits under light microscope indicated that the wall of atherosclerotic CCA was thicker than that of nonatherosclerotic CCA. The difference between the thickness of atherosclerotic and nonatherosclerotic CCAs was significant. SEM analyses showed that in nonatherosclerotic CCAs, the effect of temporary aneurysm clips was seen after 10 minutes, but in atherosclerotic CCAs, the effect was seen within the 1st minute of clipping and continued in the 5th and 10th minutes. Conclusion The duration of temporary clipping should be decreased for the neurovascular surgery of atherosclerotic patients.