Sociocultural characteristics corresponding to the ethnic origin could define individual differences in anthropometry, diet and patterns of physical activity and thus influence predisposition to obesity. The goal was to identify differences in anthropometric profile, quality of diet and patterns of physical activity among obese schoolchildren with or without indigenous ethnic origins in the region of Arica and Parinacota, Chile. Weight, clothing size, BMI, waist circumference and percentage of body fat were measured in 95 obese schoolchildren (11-12 years of age) from four schools in the northern sector of the city of Arica. Participants were consulted about their ethnic origin and questionnaires were used to evaluate quality of diet and patterns of physical activity. The results showed that obese schoolchildren presented no differences in anthropometry and patterns of physical activity on the basis of ethnic origin. However, subjects of indigenous ethnic origin disclosed a better quality of diet (p = 0.022) than those without such ethnic origin. Analysis of the sample by gender showed women to have greater weight and body fat than men, who reported higher patterns of physical activity than women. These findings were in both cases independent of ethnic origin. Participants of middle socioeconomic status were found to have higher weight, clothing size and waist circumference than those of low-middle status. It is concluded that the obese schoolchildren of indigenous ethnic origin in Arica and Parinacota have a higher quality of diet than those without such ethnic origin.