We investigated the prevalence of migraine (MIG), tension-type headache (TTH), and chronic headache in a population-based sample in Germany. A total of 18,000 subjects aged between 18 and 65 years were screened from 2003 until 2005 using a validated questionnaire. Overall 9,944 participants (55.2%) responded (mean age 43 ± 13.1 years, 52.7% women). Headache frequency <15 days/month was reported by 5,350 (55.5%) subjects of whom 1,601 (16.6%, [95% confidence interval (95% CI): 15.9–17.4]) reported episodic MIG, 1,202 (12.5%, 95% CI 11.8–13.1) episodic TTH, and 1,150 (11.9%, [11.3–12.6]) episodic MIG + episodic TTH, 1,396 (14.5%, [13.8–15.2]) unclassifiable headache. In women, episodic MIG peaked between 36 and 40 years, episodic MIG + TTH between 18 and 35 years and episodic TTH between 56 and 66 years. In men, episodic MIG was predominant between 36 and 45 years, episodic MIG + TTH between 26 and 35 years and episodic TTH showed comparable frequency between 36 and 66 years. Headache ≥15 days/month was reported by 2.6% (n = 255, [95% CI 2.3–3]). Chronic MIG was reported by 1.1% (n = 108, [0.91–1.33]), chronic TTH (n = 50, [95% CI 0.4–0.7]), chronic MIG + TTH 0.8% (n = 74, 95% CI 0.6–0.9) and unclassifiable headache 0.2% (n = 23, [95% CI 0.1–0.3]). Chronic headache was more frequent in women compared to men with the highest prevalence between 46 and 65 years. It is of note that the number of subjects with chronic headache is small in all age groups. The results of our large, population-based study provide reliable, age- and sex-specific estimates of the prevalence of primary headache disorders in Germany. The prevalence with respect to episodic and chronic primary headache disorders in Germany is comparable to other European countries and the USA.