Introduction: cervical cancer is the second most common cancer among women in the developing countries and the seventh commonest cancer in the developed countries. Human papillomavirus (HPV) is now known to be the main factor in the aetiology of cervical cancer with over 99.7% of cases being associated with previous high risk HPV (hrHPV) infection. This study was aimed to determine the prevalence and risk factors for genital hrHPV infection among women attending the out-patient clinics of the Lagos University Teaching Hospital.

Methods: this was a cross-sectional study involving a total of 200 women. Questionnaires were administered to collect data such as sociodemographic, reproductive and sexual histories. Endocervical swab samples were then taken from each participant. Samples were analyzed by polymerase chain reaction (PCR) using consensus primers targeted against the hrHPV viruses.

Results: the prevalence of hrHPV in the study was 36.5%. The most predominant HPV subtypes were 31 (25.0%), 35 (8.0%) and 16 (3.5%) with the largest proportion (76.1%) of the tested samples being positive for only a single hrHPV subtype. The study showed statistically significant associations between early age at coitarche (P = 0.032) and increasing number of lifetime sexual partners (P = 0.001) with genital hrHPV infection.

Conclusion: the prevalence of hrHPV was high in Lagos with the majority of test positive samples having only a single HPV genotype. We demonstrated early age of sexual debut and increasing number of lifetime sexual partners as the most important factors associated with genital hrHPV infection.