Background: Chilean aboriginal ethnic groups (mapuche and aymaras) have a very low prevalence rate of type 2 diabetes. The investigation of a possible relationship between this low prevalence of diabetes and obesity, hypertension and serum lipid profiles in both groups is worthwhile. Aim: To study the prevalence of obesity, hypertension and lipid profile in two Chilean aboriginal communities. Subjects and Methods: The prevalence of obesity, hypertension, fasting serum total cholesterol, HDL cholesterol, triglycerides, glucose, insulin, leptin and oral glucose tolerance test were measured in 345 mapuche (106 male) and 247 aymara (100 male) individuals. Results: Sixty three percent of mapuche women, 37.9% of mapuche men, 39.7% of the aymara women and 27.0% of aymara men had a body mass index over 27 kg/m2. Twenty percent of mapuche men, 18.0% of mapuche women, 9.0% of aymara men and 4.8% of the aymara women had high blood pressure values. Serum HDL cholesterol was below 35 mg/dl in 16% of mapuche women, 14% of mapuche men, 25% of the aymara women and 27% of aymara men. No differences in total cholesterol levels were observed between mapuches and aymaras. Conclusion: Mapuche women have higher prevalence of obesity and high blood pressure than aymara women. Low serum HDL cholesterol has a higher prevalence among aymara individuals.