(1) Background Cerebral revascularization is necessary to treat intracranial arterial stenosis caused by moyamoya disease, atherosclerosis, or large complex aneurysms. Although various donor vascular harvesting methods have been reported safe, there are no reports on the histological evaluation of donor vessels for each disease, despite the variety of diseases wherein vascular anastomosis is required. (2) Methods Pathological findings of the superficial temporal artery (STA), radial artery (RA), occipital artery (OA), and saphenous vein (SV) harvested at the institution were analyzed. Patients classified according to aneurysm, atherosclerosis, and moyamoya disease were assessed for pathological abnormalities, medical history, age, sex, smoking, and postoperative anastomosis patency. (3) Results There were 38 cases of atherosclerosis, 15 cases of moyamoya disease, and 30 cases of aneurysm in 98 donor vessels (mean age 57.2) taken after 2006. Of the 84 STA, 11 RA, 2 OA, and 1 SV arteries that were harvested, 71.4% had atherosclerosis, 11.2% had dissection, and 10.2% had inflammation. There was no significant difference in the proportion of pathological findings according to the disease. A history of hypertension is associated with atherosclerosis in donor vessels. (4) Conclusions This is the first study to histologically evaluate the pathological findings of donor vessels according to disease. The proportion of dissection findings indicative of vascular damage due to surgical manipulation was not statistically different between the different conditions.