There is still a controversy regarding the relationship between sleep apnoea syndrome and headaches, especially morning headaches. Our objectives were: (i) to compare the prevalence and the clinical data of headaches in sleep apnoea syndrome (SAS) and control (snorers) groups defined by polysomnographic recording; (ii) to analyse the clinical improvement of headaches with appropriate treatment; and (iii) to correlate headaches with mood disorders, and nocturnal respiratory and architectural sleep parameters in order to understand the underlying pathophysiological mechanisms. This is a prospective study of 324 consecutive patients referred to our sleep centre for snoring. Of these, 312 patients who underwent sleep polysomnography were finally included. Patients and controls were interviewed about their medical past, headache history and clinical characteristics, their daytime sleepiness (Epworth's sleepiness scale) and their mood disorders (Zerssen's scale). Follow-up of patients with headaches (SAS and control groups), treated or not, was also assessed. According to our definition of SAS, patients were dissociated in SAS (n=164) and snorers (n=148). Fifty-three SAS patients had headaches, of whom 58.5% (n=30) suffered from morning headaches. However, there was no statistical difference between the two groups concerning the prevalence and the clinical characteristics of headaches. In addition, headaches and morning headaches were not correlated with nocturnal respiratory and architectural sleep parameters, nor with excessive daytime sleepiness, but were strongly correlated with mood disorders. In 36 SAS patients, headaches improved under treatment, but this was not statistically different from what was found among untreated snorers. Headaches and morning headaches are common in patients with SAS but may be considered as a non-specific symptom. The underlying mechanisms are not fully elucidated but depression could play an important role. Despite this absence of specificity, the treatment of SAS, especially nasal continuous positive airway pressure, leads to an improvement in headaches in several cases.