Background: Many patients present to otorhinologists daily complaining of headache due to rhinosinusitis which generally has a specific findings. Nonetheless, isolated sphenoiditis is a rare type of sinusitis, but associated with more serious complications due to its contiguity with vital intracranial structures, and is usually associated with non-specific findings that may be missed as a cause of headache. Objectives: To highlight cases with headache due to isolated sphenoiditis that present with non-specific signs and symptoms of sinusitis, and to discuss the best methods of diagnosis and treatment to avoid serious complications. Patients and methods: A case series study of 27 patients (21 males, 8 females) aged between 18-32 years-old (mean age 25 years old), were evaluated during the period between June 2015 and December 2017 in the author's private clinic at PAR Hospital, Erbil, Iraq. Those patients were misdiagnosed as cases of primary headache (migraine or tension-type headache). The diagnosis of isolated sphenoiditis in those patients was based on clinical findings, nasal endoscopy and it was proved by computerized tomography scan. Results: The study was performed on adult patients, half of them were between 24-28 years-old, with a male to female ratio of 7:3. Headache was the presenting symptom with minimal expression of other symptoms of sinusitis, i.e.; nasal obstruction in 10 patients (37%), postnasal discharge in 5 patients (18.5%), visual symptoms in 3 patients (11%) and sneezing and itching in 6 patients (22%). Nasal endoscopic findings were negative in 5 patients (18.5%), while septal deviation was noted in 14 patients (52%), concha bullosa in 1 patient (3.7%), postnasal discharge in 5 patients (18.5) and granular pharyngitis in 10 patients (37%). Computerized tomography scanning of the paranasal sinuses was performed for all patients and proved the diagnosis of isolated sphenoiditis. Headache was relieved by medical treatment in 22 patients (81.5%). Five patients (18.5%) required surgical treatment. Conclusion: Although it is uncommon, isolated sphenoiditis must be suspected in patients with headache. It is a potentially dangerous disorder due to the contiguity of the sinus with vital neuro-vascular structures. Therefore, ENT specialists must be alert of this rare condition and radiological examination of paranasal sinuses should always be performed in prolonged and intractable cases of headache. Computerized tomography scan is the best tool in diagnosis and follow up of such cases.