Rural populations living in the northern Ecuadorian Amazon (NEA) experience the highest health burden of any region in the country. Two independent studies of colonist and indigenous groups living in the NEA are used to compare their morbidity and mortality experiences. Colonist data are from a probability sample of land plots in 1999, while indigenous data are from a representative sample of the five largest ethnicities (Quichua, Shuar, Huaorani, Cofan, Secoya) collected in 2001. Poisson regression was used to compare morbidity. Results indicate clear differences in health between populations. Indigenous groups had 30% higher probability of mortality and 63% higher incidence rate of all-cause morbidity compared to colonists. Vector-borne, chronic, gastrointestinal, and diseases of unknown origin were particularly high among indigenous groups. Factors associated with morbidity varied: morbidity rates were similar for the two youngest age groups (0-4 and 5-9), but indigenous people aged 15-39 and 40+ had almost double the morbidity compared to colonists; larger households, later months of data collection and less pollution were associated with less morbidity in both groups; better infrastructure access (electricity and roads) was generally associated with lower morbidity in both groups; and associations of land use were different by group with more cultivation of perennials and fewer annuals associated with less morbidity for colonists, but more for indigenous groups. These results demonstrate the health disparities that exist among indigenous and non-indigenous populations even when living in the same geographic region. Land use itself exemplifies the cultural and contextual differences that are evident in health, since land use decisions are related to broader demographic and economic factors that influence overall ecological and human health. Ongoing population-environment and/or environment-health research needs to recognize the broader factors involved when studying relationships between population health, development and deforestation.