Little is known about the prevalence of pelvic organ prolapse (POP). We aimed to evaluate the prevalence of POP and identify its risk factors in Japan. This was a single-centre, cross-sectional study. We recruited Japanese women seen for a Pap smear from July 2018 through May 2019. After providing their informed consent, subjects were asked to complete questionnaires. Pelvic organ support was assessed using the POP quantification (POP-Q) system by an examiner. Logistic regression analyses were conducted to identify risk factors for POP. There were 1032 women aged 21 to 84years. The distribution of POP-Q stage was stage 0, 38.0%; stage I, 45.0%; stage II, 16.4%; stage III, 0.6%; and stage IV, 0%. Rates (95% confidence interval [CI]) of stage II or greater in each age group were 6.6% (2.4-10.8) in 20s-30s; 17.6% (13.3-21.9) in 40s; 17.1% (12.9-21.3) in 50s; 18.0% (12.6-23.4) in 60s; and 28.7% (19.6-37.9) in 70s and over. Multivariate analysis revealed the following risk factors for POP, with odds ratio (95% CI): body mass index [BMI] ≥ 25kg/m2, 1.63 (1.05-2.51); BMI < 18.5kg/m2, 0.40 (0.17-0.94); hysterectomy, 4.09 (1.55-10.80); ≥ 3 vaginal deliveries, 2.26 (1.19-4.28); and ≥ 1 cup of coffee per day, 0.63 (0.43-0.92). Among Japanese women undergoing routine gynaecological examinations, 17.1% (14.7-19.5) had POP-Q stage II or greater. Overweight, hysterectomy and ≥ 3 vaginal deliveries increased the risk for POP, whereas underweight and daily coffee consumption decreased it.