We studied the prevalence and short-term natural course of chronic frequent headache (CFH) in the general population and identified risk factors. In the Netherlands everyone is registered at a single general practice. We sent questionnaires to all persons (n = 21 440) aged 25-55 years, registered at 16 general practices. We compared the characteristics of 177 participants with CFH (>14 headache days/month for >3 months) with 141 participants with infrequent headache (1-4 days/month) and 526 without headache (<1 day/month). The prevalence of CFH was 3.7% [95% confidence interval (CI) 3.4, 4.0]. In 5 months, 12% showed a clinically relevant decrease to <7 days/month. In both headache groups 70% were women vs. 41% in the group without headache. Compared with the group with infrequent headache, the CFH group had more subjects with low educational level [35% vs. 11%; odds ratio (OR) 4.3, 95% CI 2.3, 7.8], medication overuse (62% vs. 3%; OR 38.4, 95% CI 13.8, 106.9), sleeping problems (44% vs. 8%; OR 8.1, 95% CI 3.6, 18.1), a history of head/neck trauma (36% vs. 14%; OR 4.0, 95% CI 2.2, 7.1), high scores on the General Health Questionnaire (62% vs. 34%; OR 2.7, 95% CI 1.3, 3.6) and more smokers (45% vs. 19%; OR 3.1, 95% CI 1.9, 5.3). We conclude that headache frequency fluctuates. CFH is common and associated with overuse of analgesics, psychopathology, smoking, sleeping problems, a history of head/neck trauma and low educational level. Female sex is a risk factor for headache, not for chronification of headache.