BACKGROUND The objectives of this study were; (1) to assess the prevalence and frequency of headache in patients referred to polysomnography (PSG) due to a clinical suspicion of obstructive sleep apnea (OSA) or another sleep disturbance and compare with a reference population, and (2) to assess the association of OSA severity with headache and headache frequency. METHODS A total of 784 participants filled in a headache questionnaire between 2003 and 2009 at the Department of Clinical Neurophysiology, Akershus University Hospital. Of these patients 477 were suspected to have OSA, and 307 had other sleep complaints. We assessed the prevalence of headache and monthly headache frequencies, as well as sleep apnea severity using an apnea-hypopnea index (AHI). The association of headache and monthly headache frequencies with PSG subgroups was assessed using multivariate logistic and ordered logistic regression analysis. RESULTS The frequency of headache was not associated with the severity of OSA. Patients referred to a sleep study for any reason had higher odds ratio (OR) for having experienced headache during the past year than population controls after adjustment for age, gender and education, i.e. patients with normal AHI had OR of 3.56, patients with OSA had OR of 3.51, and patients with other sleep disturbances had OR of 3.33. Similarly, the adjusted OR of being in a higher category of monthly headache frequency compared to controls was higher in those with normal AHI (OR 3.42), OSA (OR 3.29), and other sleep disturbances (OR 3.00). CONCLUSIONS The odds of headache and headache frequency were higher in subjects referred to a PSG for any sleep disturbance independently of OSA, compared to general population controls. However, there was no association between experiencing headache during the past year or headache frequency with OSA severity.