Background: One in five adolescents and young adults (AYA) has a chronic health condition necessitating on-going engagement with healthcare systems. Despite increasing prevalence there remains limited understanding of the burden of illness they experience. Living with a chronic illness can challenge healthy adolescent development, with the unique health and developmental issues affecting AYA requiring different responses from the healthcare system. Aims:To examine and compare the burden of illness in this group across a large range of chronic health conditions. Methods: In a dedicated health service for AYA aged 15-25 years with chronic health conditions, (13-25 years for those with substance use issues) we detail a protocol where demographics, general health, disease-specific indicators and comprehensive psychosocial variables will be collected. The health conditions include chronic gastrointestinal disease, cystic fibrosis, chronic rheumatic disease, phenylketonuria, craniomaxillofacial deformities, renal transplant patients and problematic substance use. Results will be compared to AYA without chronic illness and AYA with diabetes.Results: This protocol outlines a comprehensive screening study for AYA with a large range of chronic health conditions, inclusive of medical, mental health, impairment and quality of life variables. It will inform service planning and provide a foundation upon which allied health service requirements (e.g. psychology) can be based. Whilst currently cross-sectional we anticipate further utility in broadening outcomes to include non-physical illness-related constructs. Conclusions:The commonalities and differences between conditions will be examined to facilitate efficiencies of scale for systems and supports. Further iterations including quantifying access to allied health services will facilitate studying the impact of such interventions on treatment adherence and improving psychosocial functioning, quality of life and disease outcomes.