HPV infection is associated with cervical cancer, one of the major public health problems in developing countries. In the Republic of Congo, despite of the high age-standardized incidence rate estimated at 25.2 per 100,000 women, molecular epidemiology data on HPV infections are very limited. We investigated HPV genotypes distribution in cervical smears among patients attending the General Hospital of Loandjili, Southwest Congo. A cross-sectional hospital-based study was conducted on 321 women. Liquid-based cytology samples were collected for cytological diagnosis and HPV detection. Nested-PCR was performed using MY09/MY11 and GP5+/GP6+ primers with genotyping by direct sequencing. Type-specific PCR for HPV-6, -11, -16, -18, -31 and -33 was also used to assess multiple infections. Out of 321 women examined, 189 (58.8%) had normal cytology, 16 (5.0%) had ASCUS and 116 (36.1%) had cytological abnormalities. HPV-DNA was detected in 22 (11.6%), 6 (37.5%), and 104 (89.6%) normal cytology, ASCUS and cytological abnormalities respectively. HPV16 was the most prevalent genotype regardless of cytological status followed by HPV70 in women without lesions and HPV33 among those with lesions. HR-HPV prevalence varied significantly according to the cervical cytology (P = 0.000). Among women without lesions, two peaks of HPV infections were observed in age group less than 30 years (60.0%) and in age group 50-59 years (7.1%). Age, age of first sex, multiple sexual partners and pregnancies were the risk factors for HPV infection in women without lesions. Our findings could be used as evidence data base for future epidemiological monitoring in this region.