BACKGROUND:Coughing during bronchoscopy causes patient discomfort and may compromise procedural stability. However, its relationship with oxygen desaturation remains unclear. This study was conducted to identify factors associated with severe cough and oxygen desaturation (peripheral oxygen saturation [SpO2] ≤85%) during standalone endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). METHODS:We retrospectively reviewed 192 stand-alone EBUS-TBNA procedures performed between March 2019 and March 2024. Cough severity was assessed using a 4-point operator-rated scale and categorized as mild (scores of 0-1 point) or severe (scores of 2-3 points). Oxygen desaturation was defined as minimum SpO2 of ≤85% during the EBUS-TBNA phase after convex-probe EBUS bronchoscope insertion. Multivariable logistic regression identified independent predictors of severe cough and desaturation while considering relevant clinical and procedural variables. RESULTS:Severe cough occurred in 78 (40.6%) patients, and SpO2 ≤85% occurred in 25 (13.0%). SpO2 ≤85% was independently associated with severe cough (odds ratio [OR] 6.45, 95% confidence interval [CI] 2.26-18.40; p < 0.001). For desaturation, female sex (OR 7.73), hypertension (OR 4.05), and station #11s sampling (OR 4.50) were independently associated with SpO2 ≤85% (p < 0.05). The #11s association did not remain significant after multiple testing corrections in the exploratory station-wise analyses. CONCLUSIONS:Clinically relevant desaturation during EBUS-TBNA was strongly associated with severe cough. Female sex and hypertension were also associated with desaturation, and #11s sampling showed a clinically relevant but exploratory signal. These findings may support individualized risk assessment and procedural planning.