We compared the clinical performance of the PapilloCheck human papillomavirus (HPV) assay with that of the GP5+/6+-PCR method with an enzyme immunoassay readout (GP5+/6+-PCR-EIA) for the detection of high-risk HPV (hrHPV) types by the use of cervical samples originating from women in a population-based by the use of cervical screening cohort tested by combined cytology and GP5+/6+-PCR-EIA (POBASCAM trial). Specimens from a random sample of 1,437 controls (women ages 40 to 60 years with normal cytological findings and without evidence of cervical intraepithelial neoplasia grade 2 or higher [> or = CIN2] within up to 8 years of follow-up) and 192 cases (women ages 30 to 60 years in whom > or = CIN3 was detected within up to 3 years of follow-up) were subjected to analysis by the PapilloCheck method. When all 17 (probably) hrHPV types were taken into account, the PapilloCheck assay had a clinical sensitivity for the detection of > or = CIN3 of 96.4% (185/192 samples; 95% confidence interval [CI], 93.7 to 99.7) and a clinical specificity for the detection of > or = CIN2 of 96.3% (95% CI, 95.3 to 97.3). After restriction of the analysis by the PapilloCheck assay to the 14 hr HPV types targeted by GP5+/6+-PCR-EIA, the clinical sensitivity and clinical specificity values were 95.8% (95% CI, 92.8 to 98.8) and 96.7% (95% CI, 95.7 to 97.7), respectively. By comparison, these values were 96.4% (95% CI, 93.9 to 98.9) and 97.7% (95% CI, 96.9 to 98.5), respectively, for the GP5+/6+-PCR-EIA. When all 17 (probably) hrHPV types were included in the analysis, noninferiority score testing revealed that the clinical sensitivity of the PapilloCheck assay for the detection of > or = CIN3 was noninferior to that of the GP5+/6+-PCR-EIA (P < 0.0001), but the clinical specificity of the PapilloCheck assay for the detection of > or = CIN2 was inferior to that of the GP5+/6+-PCR-EIA (P = 0.08) when lower bounds of 90% for sensitivity and 98% for specificity were used. When the analysis was restricted to the 14 hrHPV types targeted by the GP5+/6+-PCR-EIA, both the clinical sensitivity and the clinical specificity of the PapilloCheck assay were noninferior to those of the GP5+/6+-PCR-EIA (noninferiority score test; P < 0.0001 and P = 0.007, respectively). Thus, when the findings obtained for the 14 hrHPV types detectable by the GP5+/6+-PCR-EIA are considered, the PapilloCheck assay is clinically compatible with the GP5+/6+-PCR-EIA.