Migraine is the most common cause of recurrent headache among children and adolescents resulting in missing of school and disabling their daily life. The purpose of this study is to determine the prevalence and clinical features of headache in junior high school children in Japan. In December 2004, questionnaires were sent to 14 junior high schools. There were multiple-choice type questions on headache, mainly migraine. The questionnaires were given during school hours, and 6472 answers were obtained. One thousand four hundred seventy-eight (22.8%) students experienced severe headache and 476 (7.4%) had consulted physicians. Three hundred thirteen (4.8%) were identified as having migraine based on the ICHD-II criteria, consisting of 110/3346 boys (3.3%) and 203/3126 girls (6.5%): 91 (29.1%) with aura and 222 (70.9%) without aura. In about half of the children the migraine attacks were of short duration, ranging from 1 to 3 h. There were 36 boys (1.1%) and 45 girls (1.4%) who had shorter attacks of less than 1 h, whom we did not diagnose as having migraine according to the ICHD-II criteria. Although migraine is common among schoolchildren, it is often under- or miss-diagnosed since the clinical figure for childhood migraine differs from that for adults.