Whether the prevalence of migraine is increasing is controversial. We conducted annual surveys in 1999–2001 to investigate migraine prevalence among a nationwide sample of 13 426 adolescents aged 13–15 years. Participants from five junior high schools around different regions of Taiwan completed self-administered questionnaires. The diagnosis of migraine was based on the classification criteria proposed by the International Headache Society, 1988. Data for 23 433 person-years were collected and analysed for trends in prevalence and incidence. The 1-year prevalence of migraine increased 42% during 1999–2001 (from 5.2 to 7.4%, P < 0.001). This increasing trend was demonstrated in both sexes, all ages, and all but one studied regions of Taiwan. Of note was the biggest increment of prevalence (79%) among 7th graders (students aged 13 years) through these 3 years. Annual incidence rates did not differ between 1999 and 2000 and 2000 and 2001 (6.1% vs. 5.7%; P = 0.4). One-year persistence rates of migraine diagnosis, surrogates of migraine duration, did not differ between 1999 and 2000 and 2000 and 2001 (34.2% vs. 41.2%; P = 0.1). Our study found that the prevalence of migraine was increasing in our sampled adolescents, which results from an increment starting at age 13 or younger. The prevalence of migraine in Asians might be increasing, although previous studies showed lower prevalence in this region. Children or adolescents may be more vulnerable to the environmental or societal change.