The hypothalamus forms part of the central autonomic network, regulating body homeostasis and controlling pain. To this effect, it is strongly wired to more rostral and caudal areas, in particular the brainstem periaqueductal grey, the locus coeruleus and the median raphe nuclei, all involved in autonomic and sleep mechanisms and also in the descending control of pain perception. The hypothalamus, especially its posterior regions, becomes activated during attacks of the trigeminal autonomic cephalalgias (TACs), while brainstem, especially dorsal pontine, activity shows up during migraine attacks. The hypothalamus and interconnected brainstem areas likely represent the neural sites responsible for the chronobiological features of some headaches, in particular the sleep-related attacks typical of the TACs, migraines and the hypnic headaches.