Introduction and Hypothesis <p>Flexible cystoscopy is well tolerated by women. Reprocessing of cystoscopes requires sterilization or, at least, high-level disinfection (HLD). This study aims to assess the incidence of bacteriuria after flexible cystoscopy using ortho-phthalaldehyde HLD.</p> Methods <p>This is a prospective study. Seventy-eight women undergoing diagnostic outpatient flexible cystoscopy were included. Exclusion criteria were microbiologically confirmed or acute urinary tract infection, significant urethral stricture, and bleeding disorders. Cystoscopes were reprocessed using ortho-phthalaldehyde. Pre-cystoscopic urine cultures were obtained via catheterization 3–5&#xa0;days prior. Post-cystoscopic urine cultures were obtained immediately after the procedure. No antibiotics prophylaxis.</p> Results <p>One woman (1.3%) developed post-cystoscopy bacteriuria. The overall mean age was 58.7 ± 11.2&#xa0;years; the mean BMI was 23.4 ± 3.3&#xa0;kg/m². In the non-bacteriuric cohort, the mean age was 58.87 ± 11.3&#xa0;years, 40 (51.9%) were in the older age group (&gt; 60&#xa0;years), 60 (77.9%) were postmenopausal, 69 (89.6%) were non-diabetic, 20 (26%) had a prior hysterectomy, 13 (16.9%) had previous pelvic reconstructive surgery, 10 (13%) had undergone anti-stress urinary incontinence surgery, and no woman had current pelvic organ prolapse. The most common indication for flexible cystoscopy was hematuria (<i>n</i> = 45, 58.4%). Seventy-three (94.8%) women had unremarkable cystoscopic findings. The single bacteriuric woman was 53&#xa0;years old, postmenopausal, non-diabetic, with a BMI of 22.3&#xa0;kg/m², and an intact uterus; cystoscopy was performed for interstitial cystitis.</p> Conclusions <p>The incidence of bacteriuria following flexible cystoscopy was 1.3%. Ortho-phthalaldehyde is effective for HLD in flexible cystoscopy, provided robust rinsing, drying, and exposure-tracking protocols are maintained.</p>