Hypocretins (or orexins) are two neuropeptides synthesized by neurons located exclusively in the hypothalamus. Hypocretin-containing neurons have widespread projections throughout the CNS; with particularly dense excitatory projections to monoaminergic and serotonergic brainstem centers. The hypocretin system influences a wide range of physiological processes in mammals, such as feeding, arousal, rewards and drug addiction. Recently, a number of studies in experimental animals showed that hypocretins are involved in pain modulation within the CNS, and suggested the presence of a link between these peptides and nociceptive phenomena observed in primary headaches. The aim of this review is to describe and discuss recent studies in humans suggesting a role for the hypocretin neuronal system in cluster headache and chronic migraine.