Of the 120 known human papillomaviruses (HPV), 51 HPV types infect the genital mucosa. Very little is known about the prevalence and viral load of the majority of these low-risk (Lr-) HPV types in screening populations. We determined the prevalence of 51 HPV types and three subtypes in 999 consecutive BD-SurePath liquid-based cervical cytology samples collected during routine gynecological health checks from Belgian women. This series of screening samples was enriched with ASC-US (n = 100), low-grade squamous intraepithelial lesion LSIL (n = 100) and high-grade squamous intraepithelial lesion (HSIL) (n = 97) and analyzed by BSGP5+/6+-PCR/MPG assay for 51 HPV types and three subtypes. In consecutive screening samples, any of the 54 genital HPV (sub)types was found in 37.1%; Hr-HPV types were detected more frequently (26.8%) than the 31 Lr-HPV types (16.4%) and the six possibly high-risk types (6.6%). High viral load infections were present in 17.0% of the screening population. Among the women with cytological abnormalities, the prevalence of high viral loads of Hr-HPV types increased from negative for intraepithelial lesion or malignancy (NIL/M) over ASC-US, LSIL to HSIL (5.3, 47.1, 84.2 and 91.8%, respectively). The prevalence of possibly Hr and Lr-HPV types increased from NIL/M to LSIL but declined to HSIL. From NIL/M to HSIL, Hr-HPV infections showed an increasing frequency of high viral loads compared to total DNA positivity, but the increase between LSIL and HSIL was small. Type-specific analyses revealed substantial differences between individual HPV types in these groups. Our study provides quantitative data for the whole spectrum of genital HPV in a Belgian screening population and in a representative set of women with cervical abnormalities