Migraine is a common, disabling, multifactorial, episodic neurovascular disorder of largely unknown etiology. The disease is typically characterized by recurrent attacks of headaches and associated autonomic and neurologic symptoms. Current acute and prophylactic treatment options are far from optimal and in many cases, empirically chosen. Clearly, improved treatment is desperately needed. New drug targets may emerge from molecular research as the unravelling of the molecular basis of migraine should improve our understanding of the disease, notably why patients experience attacks so frequently. The first two migraine genes discovered in families with hemiplegic migraine encode ion transporters, emphasising that dysfunction of ion transport may be an important factor in migraine. Therefore, ion transporters can be considered as novel targets for the development of future antimigraine drugs. Molecular biologic research will increasingly become important in understanding the pathophysiology of migraine and in identifying potential molecular targets for novel treatments.