Introduction Obstructive sleep apnoea (OSA) is a sleep-breathing disorder that seems likely to have long-term negative social and health consequences in children and adolescents. There are no established standard management approaches when the first line of therapy, the tonsillectomy and adenoidectomy (T&A), is not indicated or fails to address paediatric OSA (residual paediatric OSA). This protocol describes a prospective cohort study that aims to assess the effectiveness of orthodontic interventions for managing residual paediatric OSA in patients with concomitant craniofacial issues. Methods and analysis Children aged 6–16 years who with an OSA diagnosis and did not benefit from previous T&A or qualified for T&A will be recruited. Orthodontic intervention(s), when adequately indicated (maxillary expansion, mandibular advancement or maxillary complex advancement with skeletal anchored headgear), and a control (orthodontic intervention declined) cohorts will be involved. A sample size of 70 participants (n=35 per cohort) is planned. Effectiveness data will be assessed through nocturnal polysomnography, a craniofacial index, sleep questionnaires and medical records. Additionally, the association of residual OSA and two comorbidities, obesity and asthma, will be investigated through assessing blood, urine and saliva metabolites. The changes on body mass index will also be investigated as a secondary outcome. Other additional outcomes, including association between residual paediatric OSA and periodic limbs movement, restless leg syndrome, insomnia, and the use of abiometric shirt to sleep monitoring purposes will also be considered. All participants will be followed up for 12 months after treatment allocation. The effectiveness of the intervention will be analysed by the assessment of sleep parameters, medical history (from medical chart reviews), questionnaire responses, craniofacial characteristics and metabolomic markers using an algorithm to be developed. Ethics and dissemination This study was approved by the Health Research Ethics Board-Health Panel, University of Alberta, Edmonton, Canada (Pro00084763). The findings will be shared with scientific and patient content-specific social network communities to maximise their impact on clinical practice and future research in the study topic. Trial registration number NCT03821831; Pre-results.

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