Aim: To determine the prevalence of MS in Mapuche individuals living in urban and rural environments in Chile and to investigate whether the prevalence and risk of MS in urban and rural environments differs by sex, age and nutritional status. Material and Methods: A total of 1077 Mapuche participants were recruited from urban (MU = 288) and rural (MR = 789) settings. Body mass index, waist circumference and blood pressure were measured. A fasting blood sample was obtained to measure serum glucose, HDL cholesterol and triacylglycerol. The prevalence of MS was determined using the unified IDF and ATP-III criteria. Results: An environment and sex interaction was found for the prevalence of MS (p = 0.042). The prevalence was significantly lower in male MR (13%) compared to other groups (22, 23 and 25% among female MR, female MU and male MU respectively). Also, the prevalence of central obesity and low HDL-cholesterol were significantly lower in male MR. MU are at an increased risk of developing MS compared to MR, with an odds ratio of 1.59 (95% confidence intervals 1.1 to 2.2). This risk increases along with age or body mass index of the population. Conclusions: The adoption of an urbanized lifestyle increases the risk of developing MS in Mapuche individuals. This risk is enhanced by age and nutritional status.