Introduction: The study aimed to compare pain scores during flexible cystoscopy among male patients in different positions: supine position versus lithotomy position. Methods: This prospective randomized controlled trial included male patients undergoing flexible cystoscopy at a tertiary care hospital. The pain level was assessed immediately after the procedure using the visual analog pain scale, and the cystoscopic time was recorded. Results: This randomized study involved 142 male patients undergoing flexible cystoscopy, equally divided into two groups as 71 men in the supine and 71 men in the lithotomy position. Baseline characteristics including age, indication for the procedure, prior cystoscopy experience, and surgeon background showed no significant differences between the groups. Patients in the supine position reported significantly lower pain scores compared to those in the lithotomy position (median pain score: 1 vs. 2; p < 0.001). Moderate to severe pain was significantly more common in the lithotomy group (28.2% vs. 7.0%; p = 0.002). The procedural duration was also significantly shorter in the supine group (138 vs. 180 s; p = 0.001). Multivariate analysis revealed that patient positioning was the only independent factor associated with moderate to severe pain, while other factors such as time taken to complete the procedure, previous cystoscopy history, surgeon experience, and different individual surgeons were not statistically related. Conclusion: Patients in the supine position reported reduced pain levels with a shorter flexible cystoscopy procedure duration compared to those in the lithotomy position.

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