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Cervical cancer, primarily caused by Human Papillomavirus (HPV) transmission through sexual contact, necessitates comprehensive strategies to combat its impact on women's health. Yet, certain underserved populations, such as low socioeconomic and ethnic minority groups, encounter barriers in accessing timely interventions and early diagnosis. This cross-sectional study was conducted with the aim of assessing HPV prevalence, genotype distribution, and co-infections among 280 adult women residing in a Colombian Indigenous Reserve within the Amazon region. The research adhered to a community-centric approach that respected cultural norms, native languages, and Indigenous authorities' permission. The study revealed an overall HPV infection prevalence of 31.1% (n = 87, 95% CI 25.7–36.8), with 22.5% (n = 63, 95% CI 17.7–27.8) of women infected by at least one high-risk HPV genotype and 15.0% (n = 42, 95% CI 11–19.7) infected by at least one LR genotype. These results align with the findings of other Colombian studies. Notable high-frequency genotypes included 16, 52, 66, 56, and 68, with the most common combinations being [66–52] and [66–58]. The study also assessed the prevalence of HPV vaccination, revealing a rate of 22.9%, lower than the national average. In vaccinated women, the prevalence of genotypes 16 and 18 was significantly reduced, as anticipated. Importantly, it was observed that 57.1% of all high-risk HPV infections could have been prevented with the use of the nonavalent vaccine. These findings underscore the critical need to enhance adherence to early cervical cancer detection and monitor positive cases to evaluate high-risk HPV persistence. Efforts should be directed toward continuing vaccination coverage against high-risk HPV 16 and 18 with the quadrivalent vaccine, while also striving to make the nonavalent vaccine accessible for inclusion in large-scale public health programs. Additionally, the study did not identify a specific pattern of co-infection. The study emphasizes the significance of adopting a locally tailored epidemiological approach to guide and promote cervical cancer prevention efforts in Indigenous communities. [ABSTRACT FROM AUTHOR]