PURPOSE: Headache is a common neurological condition for children to seek for medical care. The underlying causes of headache include migraine, tension type headache, intracranial masses, and sinusitis and so on. The study was aimed to analyze the clinical findings and the results of neuroimaging studies in children with headache. METHODS: A total of 120 children with headache were involved in the study who replied to the questionnaires at the department of pediatrics of Soonchunhyang University Hospital from March 2006 to October 2012. We evaluated the causes of headache by MRI scans and classified them based on the International Classification of Headache Disorders (2nd Edition, ICHD-II), 2004. RESULTS: Thirty one out of 120 children (25.8%) were classified as secondary headache with abnormal MRI findings such as sinusitis, pineal cyst, venous angioma, demyelinating disease and 89 (74.2%) patients were classified into primary headaches. Migraines without aura were diagnosed in 43 (48.3%) patients, migraine with aura in 18 (20.2%) patients, and tension type headache in 21 (23.6%) patients respectively. There was no significant difference on the median age between the patients with primary (10.5 years) and secondary (9.13 years) headache. When compared by gender ratio, primary and secondary headaches were 1.34:1 and 2.1:1 respectively. CONCLUSION: The correct diagnosis of headache may not be simple due to a variety of presentations of headache in children. We therefore have to pay a close attention to their complaints and get the neuroimaging study done if necessary.