Human papillomavirus (HPV) is the most common viral infection of the reproductive tract and can cause cervical cancer, along with other types of cancer and genital warts in both men and women worldwide. In the Sultanate of Oman no data exist on the population prevalence of, or risk factors for, (HPV) infection. It is documented that persistent infection with high-risk (HR) HPV causes cervical cancer, the fourth most frequent cancer affecting women in Oman. The aim of this study was to assess the prevalence and genotype distribution of HPV in Omani women attending gynaecology clinics in two tertiary hospitals. HPV prevalence was correlated with risk factors and other demographic data. 258 cervical samples were obtained from exclusively Omani women aged 18-68 years from the general population of Oman. HPV DNA detection and genotyping was done using Seegen assay (Anyplex II HPV28) a new multiplex real time-polymerase chain reaction (RT-PCR) assay which is based on a novel detection method. This kit detects 28 HPV genotypes simultaneously, with 19 high risk (HR) HPV and 9 low risk (LR) HPV. The results showed that HPV DNA was detected in 46 women (17.8%), and 22 different HPV genotypes were detected, comprising 15 (HR) genotypes (16, 18, 31, 33, 35, 39, 51, 52, 53, 56, 58, 66, 68, 82, and 73) and 7 (LR) HPV (6, 11, 54, 44, 43, 42, and 70). HPV prevalence rate was identified in women with normal cytology (17%) and in women with abnormal cytology (35.3%). HPV 54 was the most frequent low-risk genotype among women with normal cytology (14%) followed by the high risk HPV 82 (10%). Amongst the 46 positive cases, 58.7% were infected with HR HPV and 32.6% were infected with LR types. HIV (Human immunodeficiency) patients and oral contraceptives users showed significant association with HPV infection. The overall HPV prevalence in Omani women was 17.8%. The most frequently observed HPV types were LR HPV 54 and HR HPV 82. These are useful baseline data for health authorities in the sultanate to determine the potential impact of preventive measures including the use of prophylactic vaccines to reduce the burden of cervical cancer.