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AIMS AND OBJECTIVES The purpose of this study was to investigate the adverse effects of non-intubated suctioning. BACKGROUND Airway hygiene aims to maintain a patent airway to ensure adequate ventilation. Nasopharyngeal, oropharyngeal or nasotracheal suctioning may be used in patients who require airway suctioning but do not have an artificial airway. However, no studies till date provide insight into the adverse effects of non-intubated airway suctioning. DESIGN A clinical data-based retrospective design. METHOD Using institutional and clinical databases of three university hospitals in 2008-2016, we conducted a study with a propensity score matching method of 3,326 hospitalised patients who had undergone suction therapy with or without a tracheotomy. Conditional logistic regression analyses were performed to investigate the link between suctioning and the probabilities of adverse effects. STROBE checklist was used to report the current study. RESULTS Patients who required nasopharyngeal, oropharyngeal or nasotracheal suctioning had a higher risk of gastrointestinal ulcers than tracheotomised patients (adjusted OR 1.99; 95% CI, 1.24-3.20). Patients who received non-intubated suction had a higher risk of developing pneumonia (adjusted OR 1.59; 95% CI, 1.26-2.00), and the risk of aspiration pneumonia was three times higher than tracheotomised patients (adjusted OR 3.04; 95% CI, 1.40-6.60). CONCLUSIONS Non-intubated patients who require suctioning for airway clearing are more susceptible to gastrointestinal ulcers, pneumonia and aspiration pneumonia. The findings would facilitate in alerting healthcare professionals to this group of patients. However, more clinical research is needed to elucidate the mechanisms of adverse effects in non-intubated patients who require suctioning. RELEVANCE TO CLINICAL PRACTICE The adverse effects of suctioning can easily be overlooked in debilitated patients with no intubation. Professionals must be aware of the discomfort and risks that patients may experience.