HPV epidemiological and vaccine studies require highly sensitive HPV detection and genotyping systems. To improve HPV detection by PCR, the broad-spectrum L1 based SPF(10) PCR DEIA LiPA system and a novel E6 based multiplex type-specific system (MPTS123) using Luminex xMAP technology were combined into a new testing algorithm. To evaluate this algorithm, cervical swabs (n=860) and cervical biopsies (n=355) were tested with a focus on HPV detected by the MPTS123 assay (HPV-16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, -6 and -11). Among the HPV positive samples, identification of individual HPV genotypes was compared. When all MPTS123 targeted genotypes were taken together a good overall agreement was found (κ = 0.801, 95% CI: 0.784-0.818) with identification by SPF(10) LiPA, but significantly more genotypes (P<0.0001) were identified by the MPTS123 PCR Luminex assay, especially for HPV-16, -35, -39, -45, -58, and -59. An alternative type-specific assay was evaluated, based on detection of a limited number of HPV genotypes by type-specific PCR and a reverse hybridization assay (MPTS12 RHA). This assay showed similar results as the expanded MPTS123 Luminex assay.These results confirm the fact that broad-spectrum PCRs are hampered by type competition when multiple HPV genotypes are present in the same sample. Therefore, a testing algorithm combining the broad-spectrum PCR and a range of type-specific PCRs offers a highly accurate method for the analysis of HPV infections and diminishes the rate of false-negative results, which may be particularly useful for epidemiological and vaccine studies.