We conducted a randomized clinical trial on 32 subjects in 2 groups with chronic diseases of the sphenoid sinus (each consisting of 16 patients) to evaluate CT navigation during Functional Endoscopic Sinus Surgery. All patients registered in our study met the widely accepted criteria to be treated with FESS. 16 patients were operated on with FESS with CT navigation while 16 patients were operated on with FESS without navigation. The result drawn showed no significant statistical difference in the outcome of the operations when we used the CT navigation during FESS compared with the time we did not use it. However, we believe it is an asset to the ENT surgeon in difficult and critical operations like the sphenoid sinus surgery as it brings precision and peace to the surgeon. We recommend using CT navigation as a useful adjunct added to the surgeon’s knowledge & experience but not as a replacement to these necessities.