The objective of this study was to estimate prevalence of headache and body pain among patients referred for suspected sleep apnoea syndrome compared with the occurrence in a large population-based study (the Nord-Trøndelag Health Study). Between 1995 and 1998, ambulatory polysomnography was successfully performed in 421 consecutive patients, 324 of whom completed a questionnaire about sleep-related habits, headache and body pain. Headache and neck pain were more likely among patients admitted for polysomnography compared with the general population (n = 41 340). In the multivariate analyses, this association was mainly restricted to those with frequent complaints (> or =7 days per month). Chronic headache (headache > or = 15 days per month) was seven times more common among individuals with and without confirmed obstructive sleep apnoea syndrome than in the general population. There was no linear dose-response relationship between headache and neck pain and severity of apnoea or oxygen desaturation. Thus, hypoxia per se is less likely to explain the high headache prevalence among patients admitted for polysomnography.