BACKGROUND Headaches and sleep problems are common complaints in the daily practice of the general practitioner. Since the relationship between headaches and sleep complaints is complex, clear models of interaction are needed for adequate diagnosis and treatment. METHODS All subjects, successively seen in a headache clinic during a defined period, were subdivided based on the time of onset of cephalalgia. Subjects who reported onset of headache on a long-term basis, during the nocturnal or early morning (before final awakening) period, were systematically studied by a headache clinic and a sleep disorders center. This subgroup represented 17% of the total headache group. RESULTS Although the results of the headache clinic study did not differentiate this subgroup from the other patients, the sleep disorders center's interviews and questionnaires demonstrated a significant impact of the sleep disorders on headache and daytime function. Nocturnal monitoring during sleep identified specific sleep disorders in 55% of the subjects with onset of headache during the nocturnal sleep period. Follow-up after treatment of the sleep disorder showed that all subjects with an identifiable sleep disorder reported either an improvement or absence of their headache. The subjects identified with periodic limb movement syndrome were mostly those who reported only an improvement in their sleep and still needed treatment for their headaches. The question of the interaction and association of sleep-related headache and periodic limb movement syndrome is unresolved. CONCLUSIONS Headaches occurring during the night or early morning are often related to a sleep disturbance.