Background: Kidney transplant recipients (KTRs) have increased risk of human papillomavirus (HPV)-related cancers, including cervical and anal cancer. In this cross-sectional clinical study, we investigated the prevalence of cervical high-risk HPV (hrHPV) and low-risk (lrHPV), risk factors for cervical hrHPV infection, and the prevalence of cervical and anal hrHPV co-infection in KTRs and immunocompetent controls. Methods: During 2016–2017, we recruited 125 female KTRs and 125 female immunocompetent controls from one dermatology department (KTRs and controls) and five nephrology departments (KTRs) in Denmark. Liquid-based cervical and anal cytology samples were tested for HPV DNA using the INNO-LiPA test and participants answered a questionnaire on lifestyle. Odds ratios (ORs) were estimated using logistic regression, adjusting for age, lifetime sexual partners, smoking, and (in models concerning anal HPV) receptive anal sex. Results: KTRs had higher prevalence of cervical hrHPV than controls (35.5% vs. 18.2; OR_adjusted = 2.9, 95% CI, 1.5–5.5). In contrast, the prevalence of lrHPV was similar in KTRs and controls (25.6% vs. 23.1; OR_adjusted = 1.2, 95% CI, 0.7‒2.3). KTRs were more likely than controls to have cervical and anal hrHPV co-infection (27.3% vs. 6.6%, OR_adjusted = 6.3, 95% CI, 2.7–15.0). Conclusions: Female KTRs had high prevalence of cervical hrHPV, and co-infection with anal and cervical hrHPV was common. Our results underline that KTRs are an important target group for preventive efforts against HPV-related diseases. (Figure presented.).