Headache is a common, but rarely voiced, complaint during space flights, usually attributed to space motion sickness (SMS). We used a specifically designed questionnaire based on the criteria of the International Classification of Headache Disorders, 2nd edn (ICHD-II). Of the 16 male and one female astronauts who participated in the survey, 12 (71%) reported having experienced at least one headache episode while in space, whereas they had not suffered from headache when on earth. There were in total 21 space headache episodes, of moderate to severe intensity in 71%. In two astronauts (12%) the headache and associated symptoms would match the ICHD-II criteria for migraine and in three (18%) astronauts for tension-type headache; in 12 (70%) astronauts the headache was non-specific. The vast majority of headache episodes (76%) were not associated with symptoms of SMS. We conclude that space flights may trigger headaches without other SMS symptoms in otherwise ‘super-healthy’ male subjects. We propose to classify space headache as a separate entity among the secondary headaches attributed to disorders of homeostasis.