Qualitative research in the health system has made tremendous developments in the last decade to better understand patient experiences. What is often overlooked, are the influences that the internal structures, policies and people have on the individuals that use health services. Institutional ethnography is a qualitative approach that aims to capture the social organization of "everyday life" at various system levels. An institutional ethnographic framework was applied to two research studies exploring how families experience care in neonatal intensive care units. Data were collected to develop a deep understanding of the social contexts that exist within institutional boundaries. This paper provides evidence that how care is organized and delivered can significantly influence patient experiences, perceptions and ultimately health outcomes. Adopting institutional ethnographic techniques as a common research method is a valuable tool for health leaders seeking to understand and develop recommendations for health system reform.