Background: Prevalence of the metabolic syndrome has been described in populations with ethnic and cultural differences. The aim of this study was to determine the prevalence of the metabolic syndrome on a population from the Andes Mountains of Peru and compare it to a sea-level population. Methods: A cross-séctional study of subjects aged 30 years old or more from the high-altitude population of San Pedro de Cajas (SPC) (13,450 feet) and the sea-level population of Rimac (331 feet) was done. The metabolic syndrome was identified according to the revised National Cholesterol Education Program definition. The prevalence of metabolic abnormalities was calculated by gender, age, and population. A multivariate analysis was done with metabolic syndrome as the dependant variable. Results: Ninety-nine subjects from SPC and 172 from Rimac were included. The prevalence of metabolic syndrome was higher in SPC (22.2% versus 16.9%; p = 0.28). Prevalence of hypertriglyceridemia was significantly higher in SPC (56.6% versus 29.7%; p < 0.001) and prevalence of high blood pressure was significantly higher in Rimac (30.8% versus 18.2%; p < 0.05). In the multivariate analysis female gender was a risk factor for metabolic syndrome (odds ratio [OR] = 4.2; 95% confidence interval [CI]: 1.76-9.15). Conclusions: We found an overwhelming predominance of females with the metabolic syndrome in both populations due to high prevalences of abdominal obesity and low high-density lipoprotein (HDL) Hypertriglyceridemia prevalence was elevated in both men and women of high altitude. Lower prevalence of high blood pressure and of high fasting glucose was found in the high-altitude natives. The prevalence and characteristics of the metabolic syndrome apparently varies among different ethnic groups and this indicates the need for more epidemiologic studies.