Background: The natural environment provides multiple ecosystem services, and thus welfare benefits. In particular, it is known that different ecosystems, such as forests, contribute to human health through different ecological interactions, and that degradation of these natural ecosystems have been linked to the emergence and re-emergence of infectious diseases. However, there is little evidence on how ecosystem conservation policies affect human health. In Chile, about 20% of national land is under protection by its national network of public protected areas. Methods: We use a database of mandatory reporting of diseases between 1999 and 2014, and considering socio-economic, demographic, climate and land-use factors to test for a causal relationship between protected areas and incidence of infectious diseases using negative binomial random effects models. Results: We find statistically significant effects of protected areas on a lower incidence of Paratyphoid and Typhoid Fever, Echinococcosis, Trichinosis and Anthrax. Conclusions: These results open the discussion about both causal mechanisms that link ecosystem protection with the ecology of these diseases and impacts of protected areas on further human health indicators. JEL Codes: Q58, Q57, Q56, Q01