Despite the high prevalence of headaches, multidisciplinary headache clinics are few and their efficacy still needs validation. We set out to describe the procedures, characterize the patients and evaluate the treatment results in Danish Headache Centre. All clinical records for patients discharged in 2002 were systematically reviewed. Diagnoses were classified in accordance with ICHD-II. Outcome results were analysed with respect to headache diagnoses, frequency, intensity, absence from work and medication use. Five hundred and five patients were included and 336 were eligible for the study. Mean age was 46 years and male/female ratio 1 : 2.4. For patients without medication overuse headache (MOH) a reduction in headache frequency (P < 0.01) and intensity (P < 0.05) was seen for frequent episodic and chronic tension-type headache (TTH), migraine, cluster and other headaches. No reduction was seen in post-traumatic headache. Absence from work decreased significantly for migraine (P < 0.001) and frequent episodic TTH (P < 0.05). For patients with MOH a reduction in headache frequency was seen for TTH and migraine (P < 0.001). A specialized headache centre is valuable in treatment of patients with complex headache disorders.