HPV are the commonest STIs and are the causative agents for genital warts. In this study, we determine the prevalence and incidence of genital warts, its risk factors and the HPV types associated with it in HIV+ and HIV- women. We recruited 852 women attending cervical cancer screening clinics in Nigeria between April 2012 and August 2013 and collected information on demographics and behavioral characteristics. Nurses conducted pelvic examinations and performed Visual Inspection with Acetic Acid/Lugol's Iodine. HPV testing was done on cervical exfoliated cells using Roche Linear Array Genotyping Kit. Logistic regression models were used to identify risk factors. The point prevalence of genital warts at baseline was 2.7% (23/852). The baseline prevalence rates were significantly higher among HIV+ women (5.2%, 19/363) than HIV- women (0.8%, 4/489) (OR 6.70, 95% CI: 2.19 to 27.3, P = 0.0001). Risk factors for prevalent genital warts were HIV infection, abnormal cervical morphology on VIA/VILI and inconsistent use of condoms during sexual intercourse. Baseline HPV genotyping result is available on 278 participants of whom 9 (3.2%) had prevalent genital warts. hrHPV was detected in 5 participants, of whom 2 had multiple hrHPV infection. lrHPV was detected in 5 participants with multiple lrHPV infection in 4. Of the 5 individuals infected with hrHPV, 4 were co-infected with lrHPV. Among 239 women followed up over 6 months (contributing 1598 person months), incidence rate of genital warts was 3,003 cases per 100 000 person years (95% CI: 2,897 to 3,112). There was no association between incident genital warts and HIV status in this study (Incident risk ratio 3.23, 95% CI: 0.34 to 30.7, P = 0.28) Genital warts are common among the population sampled. Several participants with genital warts had multiple low risk and high risk HPV infections. Given that genital warts are risk factors for ano-genital malignancies, further research is needed to guide policies on effective prevention and control of genital warts.