The objective was to investigate the 3-year course of secondary chronic headaches (?15days per month for at least 3months) in the general population. An age and gender stratified random sample of 30,000 persons aged 30-44years from the general population received a mailed questionnaire. All with self-reported chronic headache, 517 in total, were interviewed by neurological residents. The questionnaire response rate was 71%. The rate of participation in the initial and follow-up interview was 74% (633/852) and 87% (83/95) respectively. The International Classification of Headache Disorders was used, and then in the next step the Cervicogenic Headache International Study Group and American Academy of Otolaryngology criteria were used in relation to cervicogenic headache (CEH) and headache attributed to chronic rhinosinusitis (HACRS). Of those followed-up, 40 had headache attributed to head and/or neck trauma (chronic posttraumatic headache), 0 had CEH and 0 had HACRS according to the ICHD-II criteria, while 18 had CEH according to the Cervicogenic Headache International Study Group's criteria, and 37 had HACRS according to the criteria of the American Academy of Otolaryngology. The headache index (frequency×intensity×duration) was significantly reduced from baseline to follow-up in chronic posttraumatic headache and HACRS, but not in CEH. We conclude that secondary chronic headaches seem to have various course dependent of subtype. Recognizing the different types of secondary chronic headaches is of importance because it might have management implications.