A door-to-door population-based epidemiological study of the prevalence of migraine and headache in a sample of 3,246 people older than 15 years of age was carried out in Cuzco, a high-altitude town in the Peruvian Andes, located at 3,380 meters. Among the 3,246 screened people, there were 172 cases of migraine and 930 cases of headache, yielding a crude 1-year prevalence of 5.3% for migraine (2.3% among men and 7.8% among women) and 28.7% for headache (17.5% among men and 38.2% among women). Our results suggest that migraine prevalence in Cuzco is close to that of other developing countries, whereas headache prevalence may be higher than in other developing countries. Multivariate logistic regression suggested that both migraine and headache were related to the female sex, age, and anxiety and/or depression. This study suggests that migraine is a relatively common disorder in Cuzco, but does not show any difference which could significantly related to altitude. In contrast, our results suggest that headache may be more frequent at high altitude than at sea level.