HIV-infected women have a high prevalence of Human Papilloma virus (HPV) infection and are more likely to be infected with high risk genotypes with the potential of progressing to cervical cancer. There is paucity of data regarding the prevalence of sexually transmitted HPV infection among HIV positive women in Nigeria. The objective of this cross-sectional prospective study was to determine the prevalence of high risk HPV and cervical squamous intraepithelial lesions among HIV positive and negative women in LUTH, Lagos, Nigeria. A combination of PCR and flow through hybridization method was used in the genotyping of HPV from samples obtained from 98 HIV positive and 97 HIV negative women. Cervical smears were also obtained using Liquid Prep medium. Statistical significance was determined using chi square test, student t-test and Fisher exact test. The prevalence of HPV among HIV positive women was 44.9% while the prevalence of high risk types was 37.5%. The commonest high risk types seen were types 31, 52, 53 and 35. The prevalence of HPV among the HIV negative women was 11%. The commonest high risk types 1 seen were types 18, 16, 52 and 56. The HIV positive women also had increased prevalence of cervical cytologic abnormalities. In view of the high prevalence and diversity of HPV genotypes among the HIV positive women, adequate screening protocols should be put in place for screening this category of women. Studies should also be carried out to determine the efficacy of existent HPV vaccines on this group of women.