Background: High altitude renal syndrome has been described in populations with excessive erythrocytosis. We evaluated whether high altitude (HA) dwellers might be at increased risk for kidney disease. Methods: We performed a cross-sectional study to investigate differences in prevalence of kidney function and metabolic syndrome in healthy subjects living at HA vs. sea level (SL) without any known history of hypertension, diabetes or chronic kidney disease. Results: We examined 293 subjects, aged 40 to 60 years: 125 SL (154 m) and 168 HA (3640 m) dwellers. HA dwellers had higher serum creatinine, lower estimated glomerular function rate (eGFR) (69.5 ± 15.2 vs. 102.1 ± 17.8 ml/min/1.73 m2, p < 0.0001), more proteinuria and higher hemoglobin concentrations compared to SL subjects. HA subjects had a lower prevalence of metabolic syndrome. Hemoglobin concentrations correlated inversely with eGFR in female (p = 0.001) and male (p = 0.03) HA dwellers. Using logistic regression analysis to compare subjects with eGFR < 90 vs. > 90 ml/min/1.73 m2, a lower eGFR was associated with female gender (odds ratio adjusted: 5.65 [95% confidence interval: 2.43–13.13]; p = 0.001), high altitude (14.78 [6.46–33.79]; p = 0.001), hemoglobin (1.68 [1.16–2.43]; p = 0.001) and uric acid (1.93 [1.36–2.72]; p = 0.001). Conclusions: Dwellers at high altitude who are considered healthy have worse kidney function, a higher prevalence of proteinuria and a lower prevalence of metabolic syndrome compared to people living at SL.