Craniovertebral junction (CVJ) surgery encompasses a wide spectrum of neurosurgical procedures ranging from transoral approaches for CVJ bone anomalies to surgery for intramedullary tumours. Intraoperative neurophysiological monitoring (IONM) has been increasingly used in recent years because of its ability to prevent neurological complications during surgery. In CVJ surgery the risk of neurological injuries is related first to the positioning of the patient and then to the surgical procedure. Application of IONM during the positioning of the patient permits fast recognition of impending causes of neurological injury. During surgery, continuous IONM permits real-time assessment of the functional integrity of the spinal tracts and provides useful feedback during surgical manoeuvres. The applications of IONM are mainly related to intradural procedures, but wider application of these techniques during surgery for CVJ instability and degenerative disorders has recently been described, leading also to better understanding of the pathophysiology of spinal cord injuries. In this paper we review and discuss the principal IONM techniques used during surgery around the CVJ.