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Background: Health inequities for children with intellectual disabilities are prevalent within different health systems, and children with intellectual disabilites have shorter life expectancies than the general population, higher mortality rates before the age of 17 and have a greater risk of potentially preventable hospitalisations. A health systems approach to research in this area provides a useful means through which research can inform policy and practice to ensure people with intellectual disabilities receive equitable healthcare; however, there is a paucity of evidence regarding how to address differences that have been described in the literature to date. The overall aim of this research is to establish the extent of health inequities for children with intellectual disabilities in Ireland compared to children without intellectual disabilities with respect to their utilisation of primary care and rates of hospitalisation, and to gain a better understanding of what influences utilisation of primary care and emergency department services in this population. Methods and analysis: The design of this research adopts a multi-methods approach: statistical analysis of health data to determine the extent of health inequities in relation to healthcare utilisation; discrete choice experiments to explore General Practitioners’ decision making and parental preferences for optimal care; and concept mapping to develop consensus between stakeholders on how to address current healthcare inequities. Discussion: By applying a systems lens to the issue of health inequities for children with intellectual disabilities, the research hopes to gain a thorough understanding of the varying components that can contribute to the maintenance of such healthcare inequities. A key output from the research will be a set of feasible solutions and interventions that can address health inequities for this population.