Patients with cluster headache (CH) have a higher prevalence of sleep apnea, and a possible relationship between these two conditions has been proposed. Although patients suffering from CH attacks often wake up from sleep, sleep apnea has been suggested to be a trigger or an associated abnormality in CH. It has been proposed that regulation of the hypothalamus may be responsible for sleep apnea, and that similiarly CH is generated in the hypothalamus. However, there is evidence that CH and obstructive sleep apnea are not causal, but rather parallel processes both generated in the hypothalamus. The exact role that sleep apnea plays in the perpetuation or precipitation of CH is still to be determined. This paper discusses the proposed pathophysiological mechanisms of these two entities and the possible relationship between CH and sleep apnea.