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To clarify the causal relationship between migraine and atopic disorders in children and adolescents.Migraine headache and atopic disorders including asthma are both common functional syndromes of childhood in which nature of the relationship is still debated. Attacks may induce in both disorders upon exposure to potential triggers in genetically susceptible individuals. Clinical phenotype manifests by temporary dysfunction of target tissue mediated by inflammation triggered by specific agents. Clinical features also change after puberty because of the partial effect of female sex hormones on the process. Appropriate definition of the syndrome and differentiating from other disorders are necessary not only for correct diagnosis, but also for planning of management strategies in children. Allergic rhinosinusitis needs to be differentiated from migraine even in experienced clinics. Questioning the presence of cranial autonomic symptoms is important clue in the differential diagnosis. Atopic disorder screening is particularly required in the diagnosis of migraine in childhood and adolescents. The link between both disorders of childhood seems to be far from a coincidence and some common inflammatory mechanisms are shared.On the basis of clinical features, laboratory findings and some practical clues in children, accurate diagnosis of migraine and atopic disorders are very critical for physicians, pediatricians and algologists.