Complementary and alternative medicine (CAM) is increasingly common in the treatment of primary headache disorders despite lack of evidence for efficacy in most modalities. A systematic questionnaire-based survey of CAM therapy was conducted in 432 patients who attended seven tertiary headache out-patient clinics in Germany and Austria. Use of CAM was reported by the majority (81.7%) of patients. Most frequently used CAM treatments were acupuncture (58.3%), massage (46.1%) and relaxation techniques (42.4%). Use was motivated by ‘to leave nothing undone’ (63.7%) and ‘to be active against the disease’ (55.6%). Compared with non-users, CAM users were of higher age, showed a longer duration of disease, a higher percentage of chronification, less intensity of headache, were more satisfied with conventional prophylaxis and showed greater willingness to gather information about headaches. There were no differences with respect to gender, headache diagnoses, headache-specific disability, education, income, religious attitudes or satisfaction with conventional attack therapy. A higher number of headache days, longer duration of headache treatment, higher personal costs, and use of CAM for other diseases predicted a higher number of used CAM treatments. This study confirms that CAM is widely used among primary headache patients, mostly in combination with standard care.