Introduction <p>Patients with human papillomavirus-related gynaecological diseases (HPV-RGD) are at risk of synchronous HPV infections in other regions, including the anal canal. The primary objective of this work was to examine the prevalence of anal HPV in patients treated for HPV-RGD. Secondary objectives were to test HPV type distribution and the risk of anal infection depending on the HPV-RGD localization.</p> Methods <p>A prospective study was conducted with two groups: the research group, histologically confirmed HPV-RGD, and the control group, gynaecological diseases not related to HPV (all human immunodeficiency virus (HIV) negative). The swabs for HPV genotyping and liquid cytology (Anyplex II HPV HR Detection test) were collected from the anal canal (both groups) and the area of gynaecological disease (research group).</p> Results <p>The prevalence of anal HPV infection in the research group (<i>n</i> = 130) was significantly higher than in the control group (<i>n</i> = 100) (64.62% vs. 11%, <i>p</i> &lt; 0.05). All patients with vulva cancer (<i>n</i> = 7) and vaginal precancer (<i>n</i> = 6) exhibited anal HPV infection (<i>p</i> &lt; 0.05). The risk of anal infection in patients with cervical cancer and precancer was 64% and 61.9%, respectively (both <i>p</i> &lt; 0.05). The most common HPV types detected in the anus were 16 (53.6% of all anal HPV-positives), followed by 31 (17.9%) and 51 (14.3%). In 84.5% of cases, the same HPV type was present in the anus and gynaecological organ.</p> Conclusions <p>Patients with HPV-RGD, HIV-negative, are at risk for synchronous anal HPV infection, with type 16 being the most common. Further research is warranted to define the clinical significance of this finding and the introduction of anal cancer screening among patients with HPV-RGD.</p> Trial registration <p>ClinicalTrials.gov identifier, NCT06574087.</p>