Headache is a common occurrence among the general population. Although the pain could be a symptom of acute sinusitis, chronic sinusitis is not considered as a usual cause of headache. In addition, autonomic-related symptoms in the sinonasal region may be associated with vascular pain. Confusion regarding these symptoms could lead to an incorrect diagnosis of sinusitis. A prospective cross-sectional study was conducted at two tertiary referral centers with residency programs in otorhinolaryngology, head and neck surgery and neurology. The study included 58 patients with a diagnosis of "sinus headache" made by a primary care physician. Exclusion criteria were as follows: previous diagnosis of migraine or tension-type headache; evidence of sinus infection during the past 6 months; and the presence of mucopurulent secretions. After comprehensive otorhinolaryngologic and neurologic evaluation, appropriate treatment was started according to the final diagnosis and the patient was assessed monthly for 6 months. The final diagnoses were migraine, tension-type headache and chronic sinusitis with recurrent acute episodes in 68, 27 and 5% of the patients, respectively. Recurrent antibiotic therapy was received by 73% of patients with tension-type headache and 66% with migraine. Sinus endoscopy was performed in 26% of the patients. Therapeutic nasal septoplasty was performed in 16% of the patients with a final diagnosis of migraine, and 13% with tension-type headache. Many patients with self-described or primary care physician labeled "sinus headache" have no sinonasal abnormalities. Instead, most of them meet the IHS criteria for migraine or tension-type headache.