Neurophysiologic intraoperative monitoring (NIOM) of the glossopharyngeal and vagus nerves (CN IX and X) is often used during surgeries involving the lower brain stem. Although both of these nerves contain sensory, autonomic, and motor fibers, it is the motor fibers that are most amenable to NIOM. CN IX supplies the stylopharyngeus muscle, and CN X supplies striated muscles in the soft palate, pharynx, and larynx. Monitoring of these CN can be performed by monitoring free running and stimulated electromyography (EMG) from the stylopharyngeus muscle (CN IX) and the vocal cords (CN X). Various surface and needle electrodes can be used to monitor these muscle groups. When CN IX is monitored, CN X should also be monitored, as it is often needed to differentiate when CN IX is selectively activated. Data are accumulating noting the use of monitoring these CN in tumor surgeries involving the lower brain stem.