Despite improved national censuses and “micro-demographic” studies, demographic processes and health conditions among indigenous populations in Amazonia and elsewhere in lowland Latin America are not well understood. A new source of demographic and health data has emerged in the past decade, namely meso-scale surveys initiated and administered by indigenous organizations. These surveys offer the potential for filling information gaps, shedding light on culturally specific factors that shape demographic processes and health, and empowering indigenous organizations with data that could inform health initiatives. This article assesses the indigenous-run survey “2005 Health Analysis of the Shuar and Achuar Nations” of eastern Ecuador in which the authors were involved, which reached 1,943 households in 257 communities in Morona-Santiago Province. We present findings on fertility, migration, sanitation, and health, and assess the strengths and weaknesses of the survey. We argue that despite flaws in the survey design and implementation, this survey revealed important linkages among fertility, migration, and health. Such surveys have the potential to provide much needed detail, representativeness, and cultural specificity that macro and micro data sources cannot provide. We conclude with recommendations to improve surveys of this type.