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Background Anthropometric measures have been classically used to understand the impact of environmental factors on the living conditions of individuals and populations. Most reference studies on development and growth in which anthropometric measures were used were carried out in populations that are located at sea level, but there are few studies carried out in high altitude populations. Objective The objective of this study was to evaluate the anthropometric and body composition in autochthonous Kiwcha permanently living at low and high altitudes. Methodology A cross-sectional study of anthropometric and body composition between genetically matched lowland Kiwcha from Limoncocha ( n  = 117), 230 m in the Amazonian basin, and high-altitude Kiwcha from Oyacachi ( n  = 95), 3800 m in Andean highlands. Student’s  t -test was used to analyze the differences between continuous variables, and the chi-square test was performed to check the association or independence of categorical variables. Fisher’s exact test or Spearman’s test was used when the variable had evident asymmetries with histograms prior to the selection of the test. Results This study shows that high altitude men are shorter than their counterparts who live at low altitude, with  p  = 0.019. About body muscle percentage, women at high altitudes have less body muscle percentage (− 24.8%). In comparison, men at high altitudes have significantly more muscle body mass percentage (+ 13.5%) than their lowland counterparts. Body fat percentage was lower among low altitude women (− 15.5%), and no differences were found among men. Conclusions This is the first study to be performed in two genotyped controlled matching populations located at different altitudes to our best knowledge. The anthropometric differences vary according to sex, demonstrating that high altitude populations are, in general, lighter and shorter than their low altitude controls. Men at high altitude have more muscled bodies compared to their lowland counterparts, but their body age was older than their actual age.

Genotyped indigenous Kiwcha adults at high altitude are lighter and shorter than their low altitude counterparts