We conducted a 3-year annual questionnaire survey of the International Headache Society (IHS) migraine diagnoses among 2414 adolescents aged 13. For those with migraine without aura (IHS 1.1) at the baseline survey (n = 89), 28% and 24% retained the IHS 1.1 diagnosis at the 2nd and 3rd surveys. Only 0.5% of adolescents had a persistent IHS 1.1 diagnosis for 3 years. Of those with IHS 1.1 or migrainous disorder (IHS 1.7) (n = 449), 43% and 48% retained the IHS 1.1 or IHS 1.7 diagnosis at the 2nd and 3rd surveys. Conversion between IHS 1.1 and IHS 1.7 was common. About 5.6% of the adolescents suffered from IHS 1.1 or IHS 1.7 for all 3 years. Independent predictors for persistent IHS 1.1 or IHS 1.7 diagnosis included frequent headache (>5 days/month) (relative risk (RR) = 1.8) and pulsatile headache (RR = 1.5). The diagnosis of IHS 1.1 in adolescents was quite unstable. Conversion between IHS 1.1 and IHS 1.7 was an important cause. Factoring IHS 1.7 into the spectrum of migraine diagnoses during epidemiological surveys provides a realistic impression of the disease burden in this age group.