Cluster headaches seem to be related to the hypothalamus. The neurotransmitters serotonin and melatonin tend to be lower in people with cluster headaches.
Although cluster headaches are distinct from migraines, they are similar in many ways. Many of the drugs used to treat migraines are also used for cluster headaches, including the triptans (imitrex, naratriptan, etc).
Daylength plays a role in many cluster headaches; many sufferers tend to get headaches in a particular season, especially summer and winter. The length of days is known to affect a body's circadian rythms. Some people experience unrelenting chronic cluster headaches.
While migraines are more common in women, cluster headache sufferers tend to be men.