WebMD Answers
The cause of cluster headaches is uncertain. It may be that certain parts of the brain begin to malfunction for an unknown reason. The hypothalamus, an area located at the base of the brain is responsible for the body's biologic clock and may be the part of the brain that is the source for the headaches. When brain scans are performed on patients who are in the midst of a cluster headache, there is abnormal activity in the hypothalamus.
Cluster headaches also:
If an individual is in a susceptible period for cluster headache, cigarette smoking, alcohol, and some foods (for example, chocolate) also can be potential causes for headache.
This answer should not be considered medical advice...
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