Agenesis of the sphenoid sinuses is a very rarely encountered anatomic variation. Findings on magnetic resonance imaging can mislead the radiologist and clinician. Therefore, the gold standard for diagnosis is computed tomography (CT) of the paranasal sinuses. We present the case of a 28-year-old man who was admitted to our hospital with a 3-month history of headache. CT of the paranasal sinuses revealed isolated bilateral sphenoid sinus agenesis.