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Abstract Aims To ascertain the number of paediatric deaths (0–14 years) with an underlying rare disease in the Republic of Ireland between the years 2006–2016, and to analyse bed usage by a paediatric cohort of rare disease inpatients prior to in-hospital death. Background Rare diseases are often chronically debilitating and sometimes life-threatening diseases, with the majority (69.9%) of rare diseases being of paediatric onset. The Orphanet database contains information on 6172 unique rare diseases. Under-representation of rare diseases in hospital healthcare coding systems leads to a paucity of rare disease epidemiological data required for healthcare planning. Studies have cited variable incidence rates for rare disease, however the burden of rare diseases to healthcare services still remains unclear. This study represents a thorough effort to identify the percentage of child mortality and paediatric bed usage attributable to rare diseases in the Republic of Ireland, thus addressing a major gap in the rare disease field. Methods Retrospective analysis of paediatric death registration details for the Republic of Ireland in the 11-year period 2006–2016 from the National Paediatric Mortality Register. Data was subcategorised as Neonatal (0–28 days), Post Neonatal (29 days