Background: Kidney transplant recipients (KTRs) have increased risk of human papillomavirus (HPV)-related anogenital (pre)cancers, including anal high-grade intraepithelial lesions and cancer. Previous studies on anal high-risk HPV (hrHPV) among KTRs are sparse. Methods: In a cross-sectional study, we included 247 KTRs and 248 controls from a dermatology department and 5 nephrology departments in Denmark during 2016-2017. All participants provided an anal cytobrush sample that was tested for HPV DNA. Participants completed a questionnaire on lifestyle and sexual habits. We used logistic regression to estimate odds ratios (ORs) of anal hrHPV in KTRs compared with controls and risk factors for anal hrHPV in KTRs. Results: The anal hrHPV prevalence was higher in female KTRs (45.5%) than in controls (27.2%). Female KTRs had almost 3-fold higher adjusted odds of anal hrHPV than controls (adjusted OR, 2.87 [95% confidence interval, 1.57-5.22]). In contrast, among men we did not observe increased prevalence or odds of anal hrHPV in KTRs compared with controls (prevalence, 19.4% vs 23.6%; adjusted OR, 0.85 [95% 95% confidence interval,. 44-1.64]). Among hrHPV-positive KTRs, 63% and 52% of men and women, respectively, were infected with hrHPV types covered by the nonavalent HPV vaccine (type 16, 18, 31, 33, 45, 52, or 58). Current smoking, >10 lifetime sexual partners, history of genital warts, and among men having had receptive anal sex were risk factors for anal hrHPV in KTRs. Conclusions: Female KTRs had an increased risk of anal hrHPV compared with immunocompetent controls. Our findings indicate that pretransplant HPV vaccination should be considered to prevent anal high-grade intraepithelial lesions and cancer caused by anal hrHPV infection in KTRs. Clinical Trials Registration: NCT03018327.