Background: There is a high frequency of human papillomavirus (HPV)-induced lesions in cervix and anus of immunosuppressed patients. However, few studies have evaluated these lesions in kidney-transplanted women.Methods: This cross-sectional study examined 31 kidney-transplanted women receiving immunosuppressive therapy at the General Hospital of Fortaleza in Brazil. Cervical and anal samples were collected and preserved in order to perform liquid-based cytology and a real-time polymerase chain reaction assay detecting high-risk HPV. Results: The patients' ages ranged from 31 to 70 years (mean: 42.6 ± 10.4). The age of sexual debut varied from 14 to 30 years (mean: 19.7 ± 3.8). Cervical cytology was diagnosed as atypical in 25.8% of cases (atypical squamous cells of undetermined significance [ASC-US] in 2 [6.2%], atypical squamous cells, but unable to exclude a high-grade squamous intraepithelial lesion in 1 [3.1%], low-grade squamous intraepithelial lesion [LSIL] in 4 [12.4%], and squamous cell carcinoma in 1 [3.1%]). Anal cytology was atypical in 35.4% of cases (ASC-US in 1 [3.2%]and LSIL in 7 [21.7%]). The presence of cervical HPV was confirmed in 22.5% of patients, and anal HPV was found in 48.8% of the cases. The relative risk of atypical anal cytology in cases of atypical cervical cytology was 4.37 (1. 35-14.20). High-risk cervical HPV did not significantly increase the risk of having atypical anal cytology. However, for HPV in the anus, this was associated with a relative risk of 10.18 (1.45-71.54).Conclusion: High-risk HPV and atypical cytology are very common in the cervix and anus of kidney-transplanted women. Furthermore, the presence of HPV in an anal sample correlates with an increased risk of atypical anal cytology. HPV tests could be useful tools for identifying patients who require anal cytology.