Indigenous populations in the Americas carry a disproportionate burden of disease. Common to populations affected by health inequities is the exposure to structural factors—social, political, environmental and economic—that shape the risks for disease. We conducted a photovoice study in three Shipibo-Konibo indigenous villages in the Peruvian Amazon. Twenty-four indigenous participants consented to take part. The study found that Shipibo-Konibo villagers are exposed to a series of structural factors such as malfunctioning latrines, lack of garbage disposal systems, lack of health services, migration, and mixing with outsiders which they see as important determinants of their health. While primary health care is urgently needed among indigenous communities in this region, any public health intervention must take into account the structural forces that affect indigenous people’s health.