Information is sparse concerning the incidence and prognosis of headache in children from the general population, especially of tension-type headache. In this study, headache diagnoses and symptoms were reassessed in 122 out of 130 schoolchildren after 3 years. Nearly 80% of those with headache at first evaluation still reported headache at follow-up. Although the likelihood of experiencing the same headache diagnosis and symptoms was high, about one-fifth of children with tension-type headache developed migraine and vice versa. Female gender predicted migraine and frequent headache episodes predicted overall headache at follow-up. The estimated average annual incidence was 81 and 65 per 1000 children, for tension-type headache and migraine, respectively. We conclude that there is a considerable risk of developing and maintaining headache during childhood. Headache diagnoses should be reassessed regularly and treatment adjusted. Girls and children with frequent headache have a poorer prognosis and therefore intervention is particularly important in these groups.