OBJECTIVE: Intraoperative neurophysiological monitoring (IONM) is used to detect cerebral ischemia during carotid endarterectomy (CEA). IONM of cranial nerves during CEA has been reported anecdotally. The aim of this study was to assess the use of IONM in identifying and preventing cranial nerve damage during CEA. METHODS: Prospective and observational study from a cohort of 81 patients undergoing CEA. Cranial nerve IONM was performed using electromyography (EMG), corticobulbar motor evoked potentials (CoMEP) and mapping techniques. Responses from spinal accessory, vagus, hypoglossal and facial nerves were recorded. RESULTS: CoMEP changes were detected in 49 patients (60.4 %). Most were related to indirect retraction and normalized at the end of the procedure. In 11 (13.5 %) cases, CoMEP changes persisted at the conclusion of the surgery, and 9 (11.1 %) of them showed a postoperative paresis. All patients normalized the neurological examination within a year. Cranial nerve mapping identified functional atypical nerve branches anterior to the carotid axis. CONCLUSION: IONM is a safe and reliable tool for detecting cranial nerve injuries during CEA and may allow to assess the functionality of surgically inconvenient nerve branches. SIGNIFICANCE: IONM plays a critical role in detecting and potentially preventing cranial nerve damage during CEA leading to better surgical practices.