BACKGROUND: The mucopolysaccharidoses are a group of rare, inherited metabolic disorders. MPS II is a X-linked recessive disease, also known as Hunter syndrome. Clinical manifestations include upper and lower respiratory tract, and head and neck pathologies influencing quality of life, morbidity, and mortality. Medical and surgical intervention outcomes for MPS are reported inconsistently, creating a challenge when synthesising and contrasting evidence. This study set out to address the inconsistency in outcome measurement in this field. International recommendations for developing a core outcome set were adopted. Available data from qualitative studies and outcomes from a modified e-Delphi surveys were used to develop a list of candidate outcomes for consideration. Three consensus meetings with patients diagnosed with MPS II alongside their parents/carers were ran to help finalise a list of outcome domains. RESULTS: Survival, airway obstruction, and quality of life were outcomes identified as important to always measure in all MPS II clinical trials and/or in clinical practice. Other outcomes for younger children included swallowing difficulties, cognitive development, ability to participate in education, and communication. The adolescent group included safety of chewing and swallowing, complications of anaesthesia, sleep quality and apnoea, nasal problems, and chronic otitis media. The adult group identified sleep apnoea, and hearing, as additional outcomes to measure. CONCLUSIONS: A novel methodology for determining a core outcome set in rare diseases has been recommended. Both functional and quality of life outcomes were identified by the three age groups of individuals and/or their parents. Adoption of these sets of outcomes in future clinical trials and/or clinical practice will enable comparison of outcomes reported.