Objectives This study investigates the biological impacts of sedentism and agriculture on humans living in the high altitude landscape of the Titicaca Basin between 800 BCE and CE 200. The transition to agriculture in other global areas resulted in increases in disease and malnutrition; the high altitude of the Titicaca Basin could have exacerbated this. Our objective is to test whether the high altitude of the Titicaca Basin created a marginal environment for early agriculturalists living there, reflected through elevated rates of malnutrition and/or disease. Methods To test this, we analyzed human remains excavated from seven archaeological sites on the Copacabana Peninsula for markers of diet and disease. These markers included dental caries, dental abscesses, cribra orbitalia, porotic hyperostosis, periosteal reactions, osteomyelitis, and linear enamel hypoplasia. Results Results showed that markers of diet did not support malnutrition or micronutrient deficiencies but instead, indicated a relatively diverse diet for all individuals. Markers of disease also did not vary significantly but were common, indicating circulation of pathogens or chronic bodily stress. Conclusions We interpret these results as an indication that while diets remained nutritious, investment in the landscape exposed populations to issues of sanitation and disease. The high‐altitude of the Titicaca Basin did not exacerbate the biological impacts of agriculture in terms of increased malnutrition. Additionally, disease load was likely related to problems faced by many sedentary groups as opposed to unique challenges posed by high altitude. In sum, despite the high elevation, the Titicaca Basin is not truly a marginal environment for humans.