This review introduces a qualitative methodology called institutional ethnography (IE) to healthcare professionals interested in studying complex social healthcare systems. We provide the historical context in which IE was developed, and explain the principles and terminology in IE for the novice researcher. Through the use of worked examples, the reader will be able to appreciate how IE can be used to approach research questions in the healthcare system that other methods would be unable to answer. We show how IE and qualitative research methods maintain quality and rigour in research findings. We hope to demonstrate to healthcare professionals and researchers that healthcare systems can be analysed as social organisations, and IE may be used to identify and understand how higher-level processes and policies affect day-to-day clinical work. This understanding may allow the formulation and implementation of actionable improvements to solve problems on the ground.