We analyzed the evolution of height in Colombia of cohorts born in the period 1965–1990 by ethnic groups. We found that Afro-Colombian men and women were the tallest: 6cm taller than indigenous people and 2cm taller than the rest of the population. We also found that the height gap between Afro-Colombians and others decreased during the period under study by 0.7cm for both men and women. While improvements were noticeable among the Afro-Colombians and those who chose not to be classified by ethnicity, in the case of the indigenous population only female cohorts registered an average-height increase of 1.5cm. Moreover, we found that indigenous Colombians were more likely than other ethnic groups to experience an increase in biological well-being as a consequence of an improvement in their socio-economic status, thereby reducing the average-stature gap between them and the rest of the population by 2.1 and 3.6cm for men and women, respectively.