Background: The few studies in Chile assessing the nutritional status of indigenous children show a high prevalence of stunting, excess weight and feeding problems. Aim: to compare anthropometric indices in children from indigenous and non indigenous ancestry. Subjects and methods: school children aged 6 to 8 years old, living in locations with three clear cut levels of social vulnerability were studied. Children were considered indigenous if their last names, as well as those of their parents were of Mapuche origin. Non indigenous were those whose last names were of Spanish origin. Results: four hundred and fifty indigenous and 684 non indigenous children were studied. Indigenous children from high vulnerability communities were approximately 0.5 z score shorter than those of non indigenous origin. Heights of indigenous and non indigenous children were similar in communities with intermediate and low social vulnerability. The proportion of the lower segment followed the same trend. Weight/height ratios were higher among indigenous children in the three vulnerability levels. Among indigenous children coming from areas of low vulnerability arm circumference was 1 cm broader than that of their non indigenous counterparts. Conclusions: stunting is prevalent among school children from areas of high socioeconomic vulnerability, mainly rural, and independent from ethnicity. Among indigenous school children overweight and a broader arm circumference are frequent. These results urgently call for located and specific nutrition interventions