Aims There is no consensus as to which Metabolic Syndrome (MetS) definition to use for South-American populations. The aim of this study is to compare the prevalence of MetS and abdominal obesity using different criteria in Andean adults aged 40 and older living permanently at high altitude. Methods We conducted a cross-sectional study in Chivay (Andean highlands). 237 participants were included. Anthropometric measurements, glucose and lipid assessments were done in all subjects. Adult Treatment Panel III (ATPIII) and International Diabetes Federation (IDF) criteria for MetS were used. Abdominal obesity prevalence was determined using the American Diabetes Association (ADA), IDF, and PREVENCION Study criteria. Cohen's Kappa coefficient (κ) was analyzed to assess agreement level between different criteria. Multiple regression analyses were performed to find predictors for waist circumference. Results MetS was identified in 28.7% (95%CI = 23.8–33.5) using ATPIII criteria, and 37.9% (95%CI = 32.7–43.0) using IDF criteria, with higher prevalence in women. The κ statistics for agreement between both criteria was 0.775 (95%CI = 0.690–0.859). Abdominal obesity prevalence according to ADA, IDF, and PREVENCION criteria was 35.9% (95%CI = 29.7–42.0), 75.9% (95%CI = 70.5–81.4), and 42.6% (95%CI = 36.3–49.0), respectively. Agreement between ADA and PREVENCION criteria was highest (κ = 0.859, 95%CI = 0.792–0.925). The strongest predictors for higher waist circumference values were triglycerides and BMI in women, and systolic blood pressure, triglycerides, fasting plasma glucose, and HDL-cholesterol in men. Conclusions MetS according to ATP III and IDF criteria was highly prevalent. IDF criteria identified a larger number of subjects with MetS. Different abdominal obesity criteria tended to show variation when applied to our sample population.