Background: Kidney health needs to be studied in low- and middle-income countries with populations living at high altitude and undergoing urbanization. We studied whether greater level of urbanization was associated with worse kidney function and higher hemoglobin was associated with worse kidney function at high altitude. Methods: Cross-sectional analysis of population-based studies in Peru including five sites at different altitude above the sea level and urbanization level (in decreasing order of urbanization): Lima (sea level), Arequipa (2335 m), urban Puno (3825 m), Tumbes (sea level), and rural Puno (3825 m). The exposures were urbanization and altitude as per study site, and hemoglobin (g/dL). The outcome was the estimated glomerular filtration rate (eGFR). Results: Four thousand two hundred eight people were studied: mean age was 57.4 years (standard deviation: 12.4) and 51.9% were women. In comparison to rural Puno, eGFR was similar in Lima; in comparison to rural Puno, Arequipa, urban Puno, and Tumbes had worse eGFR, for example, in Arequipa, β = -8.07 (95% confidence interval [CI]: -10.90 to -5.24). Intermediate (β = -8.60; 95% CI: -10.55 to -6.66) and high (β = -11.21; 95% CI: -14.19 to -8.24) altitude were negatively correlated with eGFR when only urban places were analyzed. At high altitude, there was a trend for a negative association between hemoglobin and eGFR: β = -1.09 (95% CI: -2.22 to 0.04). Conclusions: Apparently, higher altitude and level of urbanization, except for one highly urbanized site, were associated with worse kidney function. Our findings suggest that some of the adverse impact of high altitude on kidney function has been balanced by the lower risk conferred by rural environments.