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To estimate the prevalence of corpus uteri, cervix uteri, and ovarian malignancy in women undergoing hysterectomy or myomectomy for presumed benign indications.We conducted a secondary analysis of data from the 2014–2015 American College of Surgeons National Surgical Quality Improvement Program. Adult women undergoing hysterectomies and myomectomies without evidence for known or suspected cancer at the beginning of surgery were identified from the database. Our primary outcome measure was pathology-confirmed malignancy in the corpus uteri, cervix uteri, and ovary. We performed adjusted logistic regression analysis to examine the association of patient characteristics with the risk for malignancy.Our sample included 24,076 women undergoing hysterectomy and 2,368 women undergoing myomectomy. Malignancy of the corpus uteri was found in 1.44% (95% CI 1.29–1.59%) of the women undergoing hysterectomy. The prevalence varied considerably across surgical routes with the rate being 0.23% (95% CI 0.06–0.58%) in laparoscopic supracervical hysterectomy and 1.89% (95% CI 1.65–2.14%) in total laparoscopic or laparoscopic-assisted vaginal hysterectomy. Older women were significantly more likely to have preoperatively undetected malignancy of the corpus uteri (adjusted odds ratio 6.46, 95% CI 4.96–8.41 for age 55 years or older vs age 40–54 years). Additionally, 0.60% (95% CI 0.50–0.70%) and 0.19% (95% CI 0.14–0.25%) of the women undergoing hysterectomy were found to have malignancy of the cervix uteri and the ovary, respectively. Among patients undergoing myomectomy, 0.21% (95% CI 0.03–0.40%) were found to have malignancy of the corpus uteri with no occult cervical or ovarian cancer identified.Prevalence of occult corpus uteri, cervical, and ovarian malignancy was 1.44%, 0.60%, and 0.19%, respectively, among women undergoing hysterectomy and it varied by patient age and surgical route.