PURPOSE: Headache is a notable problem in clinical practice and a frequent symptom in children, but a systemic evaluation of the clinical course in affected patients is uncommon. The main aim of the present study is to investigate the natural course of primary headache in children after two years of diagnosis. METHODS: Based on the international classification of headache disorder(2nd edition), 51 children were diagnosed as migraine or tension-type headache from September, 2003 to October, 2005. They did not received prophylactic treatment. Their symptoms were reassessed in 42 out of 51 children 2 years after the initial diagnosis. We evaluated the condition of the patients with headache by a telephone interview with their parents. RESULTS: The diagnosed group consisted of 25 patients(59.5%) with migraine and 17 patients(40.5%) with tension-type headache. Regarding the location of the headache, the incidence of temporal area was higher in the migraine(52.0%) group than in the tension-type headache(11.8%) group. In the migraine group, 15 cases(60%) had pulsating headache, which was higher than in the tension-type headache group. At the 2-year follow up, headache-free or improvement was observed in 80.0%(20 cases) of the migraine group and 82.3%(14 cases) of the tension-type headache group. Among 14 children with positive headache family history, 12 patients(85.7%) were headache-free or improved. But there was not significant relationship between headache family history and prognosis. CONCLUSION: Primary headache had a high tendency to improve without long-term management by a 2-year follow-up in this study. Therefore, it is the way of reducing the unnecessary treatment to decide prophylactic treatment after investigating the severity or frequency of the headache using the headache diary or questionnaire.