Background: Traditional beliefs, knowledge and practices are formally integrated into the Ecuadorian health system.We sought to understand whether they are integrated in practice. Methods: Qualitative data were collected in two rural parishes in the central highlands of Ecuador through four focus group discussions (30 participants), eight key informant interviews, three participatory exercises (24 participants), structured observations of health facilities and analysis of official documents. Results: We found different levels of integration, coexistence, tolerance, and intolerance of traditional health beliefs and practices in health facilities. One parish has undergone dramatic social and cultural transformation, and the role of traditional birth attendants is limited. In the other parish, traditional indigenous norms and values persist, and traditional birth attendants are sought during pregnancy and childbirth. The degree to which traditional birth attendants, indigenous women and their families are included or excluded from public health services depends largely on decisions taken by local health professionals. Conclusions: Formal policies in Ecuador stipulate that health care should be intercultural, but the role of traditional birth attendants is not necessarily incorporated in practice. The integration of culturallyinformed beliefs and practices is critical for providing appropriate health services to members of vulnerable populations.