Introduction: Oxygen desaturation is a significant event during bronchoscopy. In this study, it was aimed to identify factors related to oxygen desaturation during flexible bronchoscopy (FB) and Endobronchial ultrasound (EBUS). Materials and Methods: From 16 April 2019 to 14 February 2020, 196 consecutive patients (146 FB and 50 EBUS) undergoing bronchoscopy were evaluated retrospectively. The patients’ oxygen saturations were monitored on admission and during the procedure by finger pulse oximetry. Desaturation was defined as saturation below 90%. Demographic characteristics, comorbidities, types of interventions, vitals before and during the procedure, amount of saturation decline, and sedative agents used were recorded. The data obtained were compared between the desaturated and non-desaturated groups in both FB and EBUS. We evaluated the risk factors for desaturation during bronchoscopic procedures. Results: The mean age of those who underwent FB was higher (62 [52-68] years vs. 55 [44-65] years, p= 0.05), and males were more frequent (54%, vs 19.2%, p< 0.001) in the desaturated group. In FB, short lavage was more frequent in the non-desaturated group (28.8% vs. 9.5%, p< 0.001). In EBUS, hypertension, diabetes mellitus and thyroid diseases were higher, and duration of procedure was longer (p= 0.02, p= 0.04, p= 0.01 and p <0.001, respectively) in the desaturated group. In both FB and EBUS, baseline SpO2 was lower (96% vs. 98% in FB, 97% vs. 98% in EBUS, p< 0.001 and p= 0.01, respectively), and SpO2 decline during procedures was higher (11% vs. 1% in FB, 18% vs. 3% in EBUS, p< 0.001, each) in the desaturated group. Conclusion: This study suggested that baseline SpO2 and SpO2 decline during procedures as well as sex, hypertension, and concomitant endocrine - metabolic diseases, duration of procedure were factors associated with desaturation in patients who had undergone FB and EBUS.