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Objectives At present, the available evidence regarding the relationship between prone position ventilation (PPV) and tracheal injury score remains inadequate. This study seeks to gain deeper insights into the relationship between PPV and tracheal injury score in intensive care unit (ICU) patients with invasive ventilation.Design A secondary analysis of a prospective cohort study.Setting Our study was conducted in a Class III hospital in Hebei Province, China.Participants Patients aged over 18 years admitted to the ICU between 31 May 2020 and 10 November 2023 with a tracheal tube and expected to be on the tube for more than 24 hours.Primary and secondary outcome measures The primary outcome was tracheal injury score, assessed via fibreoptic bronchoscopy for hyperaemia, ischaemia, ulcers and perforation. Lesions were classified as moderate, severe or confluent based on extent.Results Among the 149 selected participants, the average age was 58.4±16.2 years, with 65.8% being male. The results of adjusted linear regression showed that PPV was associated with tracheal injury scores (β: 5.33; 95% CI 3.84 to 6.82). Subgroup analysis indicated that PPV is significantly associated with an increased tracheal injury score, and this association remains consistent across different ages, sex, septic shock and non-septic shock groups, and duration of intubation <8 days and ≥8 days groups (p<0.001).Conclusions Our findings suggest PPV may be associated with tracheal injury score, highlighting a potential link between PPV and tracheal injury score.Trial registration number ChiCTR2000037842, registered 3 September 2020 retrospectively registered, https://www.chictr.org.cn/showproj.html?proj=57011.