We performed a cross sectional study in Lari (3600 m), a highland rural community from Arequipa, Peru. We evaluated a body mass index (BMI), glycemia and lipid profile in 74 over 18 year persons. The mean age was 51.7 ± 18.0 years, 62.2% were women, mean of BMI was 25.6 ± 3.7. Prevalence of hypercholesterolemia was 40.6%, "low HDL" in 77% of the population (93.5% in women vs 50% in men, p <0.001) and elevated level of LDL was 71.7%. The prevalence of impaired fasting glycemia was 27%. In conclusion, we found high prevalence of impaired fasting glycemia, hypercholesterolemia and especially "low HDL" in high altitude rural natives. These findings must be considered to realize interventions in high altitude populations to avoid future cardiovascular complications.