The risk of cluster headache (CH) is associated with the G-allele of the G1246A polymorphism in the hypocretin receptor 2 (HCRTR2) gene. First-line medication is effective in only about 70-80% of CH patients. We hypothesized that the HCRTR2 G1246A polymorphism is also of pharmacogenetic relevance in CH and may affect treatment response. We performed a prospective cohort study among 184 unrelated White CH patients. While the HCRTR2 1246G allele was significantly associated with CH in this group, treatment outcomes with triptans, oxygen, verapamil and corticosteroids remained unaffected. Our results do not support a role of the HCRTR2 G1246A polymorphism in drug responses in CH.