Introduction Navigation systems have been developed for image-guided surgery to aid several specialties, such as neurosurgery, orthopedics and most recently, otolaryngology and craniomaxillofacial surgery. In the head and neck surgery, it has been used for sinus surgery, craniofacial malformations, and tumor resections near important anatomical structures, such as the skull base, carotid artery and optic nerve, having made the procedures safer and less traumatic. Narrow spaces, anatomical variations in individual patients and blood obscuring the surgical field often challenges the surgeons, making it difficult to locate the exact position of an instrument. Material and method The aim of this paper is to compare the utility of the optic and electromagnetic navigation systems used in our clinic, especially for patients with extensive lesions. We reviewed three computer navigation systems: Stryker Intellect ENT, Medtronic Fusion and Xion Polar Matrix. Results and conclusion Navigation systems allow the surgeon to correlate anatomical landmarks with the radiographic or magnetic resonance imaging, providing an increased three-dimensional orientation intraoperatively. The advantages of navigation system consist in accurate target localization, enhanced safety and reduced risks of complications. The main disadvantages are the costs involved. The navigation system will never substitute an experienced surgeon or adequate anatomical knowledge.