Introduction HPV infection causes cancer at several anatomical sites. However, the natural history of the infection in non-cervical sites have been understudied, especially at the oral epithelium.

Methods In our study, we investigated 351 samples from three different sites of 117 patients, searching for HPV By generic and specific PCR and Microarray, and related risk factors.

Results HPV DNA prevalence was 89.5% (105/117) in the genital lesions, 53.8% (63/117) in oral samples and 59% (69/117) in anal samples. Regarding the risk factors associated with HPV in the genital lesions, we found statistically significant rates for oral (p=0.039) and anal sex practices (p=0.0000012). For oral samples, we observed a relevant correlation concerning oral contraceptive use (p=0.039), tobacco smoking (p=0.036) and alcohol use (p=0.0075) while in anal samples, we found higher risk for HPV infection in patients relating non-exclusive sexual partners (p=0.013). The presence of viral DNA in all the three sites was observed in 36.8% of the cases (43/117). Among them, 18% (21/117) presented concordant HPV genotypes, diverging from the literature, corroborating that there is still much to learn about HPV natural history, since different biological behaviours are expected within different populations.

Conclusion In our study we also evaluated if the detection of oral HPV would suggest an infection in the anogenital tract. Nevertheless, our results showed only 36.8% of correlation pointing out that it is not suitable as a an auxiliary biomarker for HPV anogenital infections.