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Availability of data and materials: The trial protocol, statistical analysis plan, and statistical report are available via the University of Cambridge data repository (https://www.data.cam.ac.uk/repository). Datasets will be available from R Fitzgerald (rcf29@cam.ac.uk) on request. Copyright © The Author(s) 2023. Background: The Cytosponge is a cell-collection device, which, coupled with a test for trefoil factor 3 (TFF3), can be used to diagnose Barrett’s oesophagus, a precursor condition to oesophageal adenocarcinoma. BEST3, a large pragmatic, randomised, controlled trial, investigated whether offering the Cytosponge-TFF3 test would increase detection of Barrett’s. Overall, participants reported mostly positive experiences. This study reports the factors associated with the least positive experience. Methods: Patient experience was assessed using the Inventory to Assess Patient Satisfaction (IAPS), a 22-item questionnaire, completed 7–14 days after the Cytosponge test. Study cohort: All BEST3 participants who answered ≥ 15 items of the IAPS (N = 1458). Statistical analysis: A mean IAPS score between 1 and 5 (5 indicates most negative experience) was calculated for each individual. ‘Least positive’ experience was defined according to the 90th percentile. 167 (11.4%) individuals with a mean IAPS score of ≥ 2.32 were included in the ‘least positive’ category and compared with the rest of the cohort. Eleven patient characteristics and one procedure-specific factor were assessed as potential predictors of the least positive experience. Multivariable logistic regression analysis using backwards selection was conducted to identify factors independently associated with the least positive experience and with failed swallow at first attempt, one of the strongest predictors of least positive experience. Results: The majority of responders had a positive experience, with an overall median IAPS score of 1.7 (IQR 1.5–2.1). High (OR = 3.01, 95% CI 2.03–4.46, p < 0.001) or very high (OR = 4.56, 95% CI 2.71–7.66, p < 0.001) anxiety (relative to low/normal anxiety) and a failed swallow at the first attempt (OR = 3.37, 95% CI 2.14–5.30, p < 0.001) were highly significant predictors of the least positive patient experience in multivariable analyses. Additionally, sex (p = 0.036), height (p = 0.032), alcohol intake (p = 0.011) and education level (p = 0.036) were identified as statistically significant predictors. Conclusion: We have identified factors which predict patient experience. Identifying anxiety ahead of the procedure and discussing particular concerns with patients or giving them tips to help with swallowing the capsule might help improve their experience. Trial registration ISRCTN68382401. The BEST3 trial was funded by Cancer Research UK (C14478/A21047), National Institute for Health Research covering service support costs, the UK National Health Service funding excess treatment costs and Medtronic providing funding for Cytosponge devices and TFF3 antibodies. RCF is funded by a Programme Grant from the Medical Research Council (RG84369) and is CI for the BEST3 trial and the Innovate UK funded DELTA study. JO was supported by PDS’s Cancer Research UK programme Grant (C8162/A16892) and is currently supported by the Barts Charity (EMSG1K1R). RM was supported by PDS’ Cancer Research UK Cancer Prevention Clinical Trials Unit funding (Grant No.: C8162/A25356). SGS is supported by a Yorkshire Cancer Research Fellowship. JW is funded by a Cancer Research UK career development fellowship (C7492/A17219). BG was funded as part of the DELTA study by Innovate UK (Grant No. 41162). FW is supported by the Cancer Research UK CanTest Grant [C8640/A23385]. RL is supported by the Intramural Research Program of the US National Institutes of Health/National Cancer Institute.