BACKGROUND: Preventable maternal and infant mortality continues to be significantly higher in Latin American indigenous regions compared to non-indigenous, with inequalities of race, gender and poverty exacerbated by deficiencies in service provision. Standard programmes aimed at improving perinatal health have had a limited impact on mortality rates in these populations, and state and national statistical data and evaluations of services are of little relevance to the environments that most indigenous ethnicities inhabit. This study sought a novel perspective on causes and solutions by considering how structural, cultural and relational factors intersect to make indigenous women and babies more vulnerable to morbidity and mortality. METHODS: We explored how structural inequalities and interpersonal relationships impact decision-making about care seeking during pregnancy and childbirth in Wixarika communities in Northwestern Mexico. Sixty-two women were interviewed while pregnant and followed-up after the birth of their child. Observational data was collected over 18 months, producing more than five hundred pages of field notes. RESULTS: Of the 62 women interviewed, 33 gave birth at home without skilled attendance, including 5 who delivered completely alone. Five babies died during labour or shortly thereafter, we present here 3 of these events as case studies. We identified that the structure of service provision, in which providers have several contiguous days off, combined with a poor patient-provider dynamic and the sometimes non-consensual imposition of biomedical practices acted as deterrents to institutional delivery. Data also suggested that men have important roles to play supporting their partners during labour and birth. CONCLUSIONS: Stillbirths and neonatal deaths occurring in a context of unnecessary lone and unassisted deliveries are structurally generated forms of violence: preventable morbidities or mortalities that are the result of systematic inequalities and health system weaknesses. These results counter the common assumption that the choices of indigenous women to avoid institutional delivery are irrational, cultural or due to a lack of education. Rather, our data indicate that institutional arrangements and interpersonal interactions in the health system contribute to preventable deaths. Addressing these issues requires important, but achievable, changes in service provision and resource allocation in addition to long term, culturally-appropriate strategies.