The objective of this study was to investigate the allelic frequency of the fat mass and obesity-associated (FTO) gene (rs9939609) and its influences on obesity and metabolic risk biomarkers in a cohort of normal weight and obese Chilean children determining its ethnicity.A total of 136 normal weight children and 238 obese children (between 6 and 11 yr old) from an urban setting were recruited for this case-control study. The children were classified as normal weight [body mass index (BMI) ≥ 5th and 95th percentile), according to the international age- and gender-specific percentiles defined by the Center for Disease Control and Prevention. The analysis of serum markers was carried out using commercial kits. The FTO polymorphism was determined through a high-resolution melting enabled real time polymerase chain reaction. Ethnicity was determined by analyzing mitochondrial DNA by the restriction fragment length polymorphism method.As much as 85% of the cohort was Amerindian. The minor A allele of rs9939609 was associated with obesity (odds ratio (OR): 1.422 [95% confidence interval (CI) 1.068-1.868] p = 0.015), calculated using an additive model. In sex-stratified analysis we found that the risk variant (A) of rs9939609 was associated with a higher homeostasis model of assessment for insulin (HOMA-IR) in prepubertal obese girls. In male carriers of the A allele, HOMA-IR showed no further deterioration than that already associated with obesity.In summary, we confirm the association of the FTO gene single-nucleotide polymorphism rs9939609 with obesity in Chilean Amerindian children. Furthermore we show an association between the risk allele (A) and insulin resistance-related markers in prepubertal obese girls.