No one knows exactly what causes cluster headaches. As with many other headache syndromes, there are many theories, many of which center on the autonomic or "automatic" nervous system or the brain's hypothalamus. These systems play a role in rhythmic or cyclical functions in your body. The involvement of either system in the syndrome would account for the periodic nature of the headache.

Many clinical experts believe that cluster and migraine headaches share a common cause that begins in the nerve that carries sensation from the head to the brain (trigeminal nerve) and ends with the blood vessels that surround the brain.

Other experts believe that the pain arises in the deep vascular channels in the head (for example, the cavernous sinus) and does not involve the trigeminal system.

Other clinical theories and possible triggers include:
Irregularities in the body's sleep-wake cycle
Alcohol (especially red wine)
Smoking
Prior head trauma
Genetics (familial cause)