There are several genital HPV DNA detection systems described, however most of them present different disadvantages regarding the number of amplified and detected types, sensitivity, type specificity. A new PCR and hybridization based detection method was developed for sensitive and balanced amplification and specific typing of HPV DNA from clinical samples. The technique amplifies and detects 46 HPV types: 2a, 3, 6, 7, 10, 11, 13, 16, 18, 26, 27, 28, 29, 30, 31, 33, 34, 35, 39, 40, 42, 43, 44/55, 45, 51, 52, 53, 54, 56, 57, 58, 59, 61, 66, 67, 68, 70, 72, 73(MM9), 74, 82(MM4), 84(MM8), 89, 90, 91. Key elements of the L1F/L1R PCR and hybridization system are: the special selection of the amplified region, a novel and optimized amplification primer set, circumspectly designed general and type-specific oligonucleotide probes. Detection following a multiplex PCR is based on solid phase hybridization in microtiter plate format using general and type-specific probes at medium stringency, which makes the detection robust in case of small sequence variations. The assay is highly reproducible and suitable for automation. The method was compared to Hybrid Capture II test, and after clarifying conflicting results, the comparison showed an excellent agreement (96.2%).