Special education for children with chronic health conditions or disabilities requires the integration of health care work with education. This phenomenon occurs in an understudied and challenging context for integrated care despite policies and protocols that outline work processes in this context. We are interested in an approach to inquiry that will allow us to address gaps in current literature and practices in integrated care, and move towards informing policy. Institutional ethnography is an approach to inquiry that maps the actualities of what individuals do at an everyday local level, while examining this work activity in relation to the sociopolitical context. It has been used to change policy and local practice by highlighting disjunctures between policy and actuality. We are adopting institutional ethnography and its three common methods of data collection: document collection, interviews, and observation/shadowing. Informants to this inquiry are chosen from school-based teams, family-centred units and constellations of clinical professionals. We are following work processes, verbally and visually mapping what is done and by whom. It is important to note that work includes 'unofficial' work, including the work of families and others who may not be assigned an official work role in a policy or protocol. The mediating role of texts in work processes is also being mapped in order to link the local work to the high-level social coordinators. To begin, analysis focuses on local, or micro-level, work processes; next, analysis identifies and explains the macro-level coordination of the local work (i.e. social and political structures). A primary outcome of this study will be the creation of verbal and visual maps that demonstrate the social organisation of work processes occurring in the health care-special education interface. These maps will make invisible work visible, highlight disjunctures between policy and practice and identify opportunities for change. They will be useful for critical knowledge translation purposes, providing parents and professionals with an awareness of how their individual work fits in to the larger picture of integrating health care work in special education.