The influence of altitude above sea level on intelligence has received only tangential attention in the literature despite that, firstly, the scarcity of oxygen occurring at high altitude impairs cognitive functioning; second, UV radiation, which is stronger at high altitude, is theorized to negatively affect intelligence; and third, the rugged terrain of high altitudes has negative effects on economic activity, which in turn affects cognitive development. This study evaluated the three potential causes using Math and Reading scores from a national census of schools that targeted children of approximately eight years of age in their 2nd year of instruction in Peru. It was limited to the 5° to 13° S latitudinal segment (N = 1073 districts). The Western and Eastern slopes of the Andes Mountains and altitudes below and above 2300 m were compared. The evidence indicates that oxygen deprivation does not explain observed negative effects of altitude on intelligence. Differences in intelligence along altitude and between Western and Eastern regions are attributable to UV radiation and the economic impacts of ruggedness. Sexual attitudes and infectious diseases in the lower Amazon region may account for an observed altitude x region interaction.