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Background Eosinophilic oesophagitis (EoE) is a chronic immune-mediated disease that significantly impacts paediatric patients and their families, often complicated by comorbid allergic conditions. Understanding parental concerns and treatment preferences is essential to foster shared decision-making and improve adherence.Objective To investigate baseline parental concerns and evolving treatment preferences for paediatric EoE, particularly after receiving targeted information about disease progression and treatment efficacy.Methods A questionnaire-based study was conducted among parents of children with EoE in Israel. Data collected on demographic and clinical characteristics, parental concerns (measured using a Likert scale) and treatment preferences under various hypothetical scenarios. Statistical analyses were performed to evaluate preference shifts and associations with parental concerns.Results Among 63 parents surveyed, baseline treatment preferences included oral medications (65.1%), elimination diets (17.5%) and subcutaneous (SC) biological therapies (17.5%). The highest parental concern was the need for chronic medication (median=5, IQR=4–5). After receiving targeted information, 68.2% of parents expressed willingness to switch to SC therapy to manage allergic comorbidities, while 56.1% considered switching due to concerns about oral medication side effects. Economic considerations influenced baseline preferences but did not deter transitions to SC therapy after targeted education.Conclusion Parental preferences for EoE treatment evolve with targeted information on efficacy and safety, underscoring the need for personalised, patient-centred care. Addressing parental concerns and enhancing communication between healthcare providers and families can optimise treatment adherence and outcomes for children with EoE.