Background:  The second most common infection-related cancers worldwide are those associated with human papillomavirus (HPV). HPV is a leading cause of cancer deaths in Nigerian women, however very little is known about its molecular epidemiology in Nigeria. We, therefore, set out to evaluate the circulating genotypes of HPV in women who had abnormal cervical cells and determine the association. Methods: Cervical swab samples were collected from 250 consenting women ages 20 - 70 years accessing cervical cancer test facilities at Jos University Teaching Hospital (JUTH), Federal Medical Centre (FMC) Keffi, and the National Hospital, Abuja (NHA), on obtaining ethical approvals. Socio-demographic/risk factors information were obtained through structured questionnaires. Samples were analyzed for the presence of both squamous intraepithelial lesions (SILs) and HPV DNA using the standard Papanicolaou staining (‘Pap' smear) and polymerase chain reaction (PCR) respectively. Type-specific primers targeting E6 and E7 oncogenes of the virus were used in nested-multiplex PCR followed by Sanger sequencing of positive amplicons. Results: The reported prevalence of HPV infection and abnormal cervical cytology was 35.6% and 15.6% respectively with a mean age ±SD of 44.5±11.9 years. Cervical cytology features identified were ASCUS (48.7%), LSIL (30.8%) and HSIL (20.5%). Women aged 40 - 49 were more likely (4.4%) to have abnormal cervical cells. In addition, 12 HPV genotypes (HPV- 6/11, 16, 18, 33, 35, 39, 42, 45, 51, 58, 59 and 66) were responsible for the abnormal cervical cells with HPV-18 predominating. Moreover, our findings revealed that HPV-18, 16, 33 and 59 were the four most frequently identified genotypes circulating among women with abnormal cytology in the population. Conclusions: These findings provided strong molecular evidence on the circulating genotypes of HPV in patients with abnormal cervical cells in Nigeria.