There is no sensitive tool to monitor embolic events and predict patients at a risk for strokes during thoracic endovascular aortic repair. We examined the relationship between the number of high intensity transient signals (HITS) by transcranial doppler ultrasound and the extent of atherosclerotic plaques in aortic arch. Thirteen patients were treated as a part of a single center United States Food and Drug Administration-approved investigational device exemption for various thoracic aortic pathologies. Bilateral transcranial doppler ultrasound transducers recorded the number of HITS. CT angiography and intravascular ultrasound were used to measure the thickness of mural thrombi and determine their arch location. All 13 patients had detectable HITS, and one patient sustained a stroke. Eleven patients had quantifiable mural thrombi. The highest HITS were observed in patients with thrombi in zones 2 to 3. All three patients with bovine arch had more HITS in the right middle cerebral artery whereas the patients with normal arch anatomy had more HITS in the left middle cerebral artery. The presence of mural thrombi in zones 2 and 3, irrespective of their thickness, was associated with increased HITS during thoracic endovascular aortic repair. This is the first study to characterize the significance of mural thrombi in aortic arch and their relationship to embolic events during aortic arch manipulations.