The effect of altitude of residence on the growth status of 11,454 indigenous school children 6–14 years of age in Oaxaca, southern Mexico, was examined. Indicators of living conditions (human development index [HDI], index of community nutritional risk [INR], index of marginalization [IM], index of relative isolation [II]) were regressed on z‐scores for height, weight and BMI, and the residuals were regressed on altitude of residence (km). Independent of other environmental conditions, altitude negatively affected height by approximately −0.07 z‐scores per kilometer altitude above sea level. The estimated average decrease in stature was 0.92 cm per kilometer elevation. BMI was significantly increased, 1.2 units per kilometer elevation, consistent with earlier studies of growth status and altitude. In contrast, weight was not affected by altitude of residence. Approximately 36% of the reduction in height and 54% of the increase in BMI were due to altitude effects; the remaining changes in height and BMI were associated with environmental factors reflected in the indices of community well‐being considered. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.