Migraine is a common, multifactorial disorder, typically characterized by recurrent attacks of throbbing unilateral headache, autonomic nervous system dysfunction and, in approximately one-third of cases, neurological transient symptoms (migraineous aura). The diagnosis of primary headaches is exclusively a clinical task but, for this reason, it is sometimes subjective and arbitrary. However, until today no single diagnostic tool is able to define, ensure or differentiate idiopathic headache syndromes, although, in the clinical setting, conventional neuroimaging techniques are often widely and improperly used in headache patients. Recent years have seen rapid growth of neuroimaging methodology which has provided new insights into functional brain organization of migraine patients. Although functional magnetic resonance imaging has today little or no value in clinical practice, clinicians role is crucial since without a proper clinical selection neuroimaging studies could generate inconclusive results. Likewise, functional neuroimaging is crucial for clinicians in order to further elucidate pathophysiological mechanisms underlying this complex and often disabling disease and to provide new therapeutical approaches for migraine patients.