The purpose of this study was to compare the frequency of microembolic brain infarcts after direct navigation method versus exchange method in carotid artery stenting and vertebral artery origin angioplasty. This is a prospective study conducted at Shiraz University of Medical Sciences in southern Iran. Consecutive patients undergoing "carotid angioplasty and stenting" and "vertebral artery origin stenting" were randomly assigned into two groups with "direct navigation method" and "exchange method." Subsequently, postprocedural magnetic resonance imaging (MRI) including diffusion weighted imaging and apparent diffusion coefficient were obtained within the first 24 hours after completion of the procedure. In total, 89 patients were recruited (67% male, mean age: 72 years). Cases comprised of 38 left internal carotid arteries (ICAs), 38 right ICAs, 6 left vertebral artery origin, and 7 right vertebral artery origin. Forty patients underwent exchange method, while 49 underwent direct navigation method. There was only one clinical stroke that occurred in "exchange method" group. Fifteen patients (37.5%) in exchange group and 23 patients (46.9%) in direct navigation group developed diffusion restricted lesions. In exchange group, 13 patients (32.5%) had at least one diffusion restricted lesion ipsilateral to the target vessel, and three patients (7.5%) had at least one diffusion restricted lesion contralateral to the target vessel. In direct navigation group, these measures were 19 (38.8%) and 9 (18.4%). However, no statistically significant intergroup differences were observed. The only significant difference was bilateral infarct percentile, which was more common in the direct navigation method (0.032). Diffusion restricted lesions were more common in the direct navigation method, both ipsilateral and contralateral to the target vessel, and in both carotid and vertebral artery study subgroups. However, differences were not statistically significant.