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Background Healthcare transition (HCT) for youth with disabilities is a complex phenomenon influenced by multiple interacting factors, including health, personal and environmental factors. Current research on the transition to adulthood for disabled youth has primarily focused on identifying these multilevel factors to guide the development of interventions to improve the HCT process. However, little is known about how this complex array of factors interacts and contributes to successful HCT. Systems thinking provides a theoretically informed perspective that accounts for complexity and can contribute to enhanced understanding of the interactions among HCT factors. The objective of this paper is to introduce general concepts of systems thinking as applied to HCT practice and research. Methods Several systems thinking concepts and principles are introduced and a discussion of HCT as a complex system is provided. Systems dynamics methodology is described as one systems method for conceptualizing HCT. A preliminary systems dynamics model is presented to facilitate discourse on the application of systems thinking principles to HCT practice, policy and research. Conclusions An understanding of the complex interactions and patterns of relationships in HCT can assist health policy makers and practitioners in determining key areas of intervention, the impact of these interventions on the system and the potential intended and unintended consequences of change. This paper provides initial examination of applying systems thinking to inform future research and practice on HCT. [ABSTRACT FROM AUTHOR]