We evaluated the effectiveness of two navigation systems with optical tracking in endoscopic sinus surgery (ESS). The Signa SP/i Intraoperative navigation system (General Electric Co., Intraoperative NS) is advantageous in acquiring both real time and high-resolution images during surgery, compared to conventional image-guided navigation (Stealth Station TREON, Medtronic Inc., IGNS) that rely entirely on preoperative three-dimensional images. We studied the following in 14 patients treated with intraoperative NS and 19 treated with IGNS: 1) additional time for navigation system implementation, 2) available instrumentations in ESS, and 3) navigation system accuracy. Navigation systems required additional time to prepare ESS. The time lapse from admittance to the operating room to ESS onset was measured in patients under both systems and controls undergoing ESS without any image guidance. Preparation of the intraoperative NS required an additional 52 min and IGNS required 17 min compared to the control group. Based on operative instruments, the intraoperative NS has some limitations arising from the application of a high magnetic field. Surgical instruments must not be attracted by the magnetic field in the operating room. So those used in our study were thoroughly examined and some remanufactured using MR safe materials. All instruments in ESS could be used in surgical guidance during surgery in the IGNS. Anatomic landmarks were accurately visualized using intraoperative NS and IGNS. Intraoperative NS renews the image during surgery, so surgeons could confirm the surgical outcome during ESS. Since the average distant error in both systems was between 1 mm and 2.5 mm, we confirmed that accuracy obtained with both navigation system was suitable for ESS completion. The intraoperative NS renewed the image during navigation. In conclusion, both navigation systems are sufficient for accurate image navigation in ESS, but navigation systems must be selected based on the individual case.