The aim of this study was to evaluate the frequency of abnormal findings in magnetic resonance imaging (MRI) in children with headache, the clinical relevance of these findings, and whether more sophisticated technologies also result in more relevant abnormal findings. The MRIs of 1004 children with age ranging from 1 to 17 years were retrospectively analyzed. Children who were investigated with established sequences (n = 419) were compared with those examined with state-of-the-art MRI acquisition technology (n = 585). In 216/1004 investigations, MRI was performed because of headache (74/216 with established sequences, 142/216 with state-of-the-art acquisition technology). In 114/216 (52.8%) patients with headache, the MRI was abnormal with relevant findings in 23/114 patients and findings without clinical relevance in 91/114 children. A higher incidence of abnormal findings than in previous reports was found but there was only limited clinical gain of information using modern sequences in children with headache.

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