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The circadian cycle is the 24-hour timekeeping system present within most living organisms. This biological "clock" allows the organism to anticipate and prepare for the changes in the physical environment that are associated with day and night. It is located in the hypothalamus where it controls the internal organization of body systems and ensures that internal changes that take place are coordinated with each other. In addition, the circadian cycle is responsible for the individual responding the "right way" at the right time of day (e.g., sleepy at night, awake during the day). The hypothalamus carries out this task by regulating hormone production of various glands in the course of a 24-hour cycle.

Some characteristics of cluster headache are indicative of a circadian pattern involvement including:

• Attacks occur at night during the first REM (rapid eye movement) cycle of sleep
• Attacks usually occur at the same time of day although there may be other random attacks in the course of the day

There are also indications that the attacks of cluster headache and the periodicity may follow a circannual cycle. A circannual cycle describes the adaptation of an organism or an individual to seasonal changes in the year. Circannual patterns of cluster headache include:

• Cycles tend to begin within several weeks of the winter or summer solstices
• Episodes for some patients regularly begin in the spring or fall.

Each patient may have their own pattern and each individual pattern has its own cyclic schedule.