BACKGROUND: Human papillomavirus (HPV) associated cancers are increasingly reported globally, including in sub-Saharan Africa (SSA). However, with the exception of cervical HPV infection, data from SSA on the epidemiology of oral and genital HPV infections are limited. This study assessed the prevalence and concordance of oro-genital and anal HPV genotype specific infections among women in the general population. METHODS: We conducted a cross-sectional study in sexually active women aged 18-45 years in Ibadan, Nigeria. After a face-to-face interview and clinical examination, oral, cervical, vulvar, and anal samples were collected from participants and tested by the Anyplex II 28 HPV assay. Descriptive and multivariable analyses were used to report prevalence and risk factors associated with HPV infections. RESULTS: The prevalence of any vulva, cervical, anal, and oral HPV infections was 68.0% (210/309), 59.7% (182/305), 56.8% (172/303), and 16.1% (14/286), respectively. There was an inverse relationship between age-group and HPV prevalence of HPV in all anatomic sites except for the oral HPV infections. HPV 35 was the most prevalent high-risk HPV genotype in the vulva, cervix and oral cavity. Associated risk factors for HPV infection in each of the anatomic sites were reported. Overall, 10.0% (31/310) women had concordance of any HPV type in the four anatomic sites. CONCLUSION: There was a high prevalence of oro-genital and anal HPV infections among sexually active Nigerian women, with concordance of HPV types in the cervix, vulva, anus and oral cavity. We advocate large longitudinal studies that will involve sampling of multiple anatomic sites and inclusion of other women in the community for better understanding of HPV epidemiology in this region.