The VALHUDES protocol was established to evaluate clinical accuracy of human papillomavirus (HPV) assays to detect cervical precancer on first-void urine (FVU) and vaginal self-samples versus matched clinician-collected cervical samples (CCSs). Here we evaluated clinical performance of Alinity m HR HPV assay in a colposcopy referral population. Home-collected FVU (Colli-Pee FV 5020) 1 day before colposcopy (n = 492), at-clinic collected dry vaginal self-samples [multi-Collect Swab (mC; n = 493), followed by Evalyn Brush (EB; n = 233) or Qvintip (QT; n = 260)] and matched CCSs, were available for the study. Sensitivity to detect cervical intraepithelial neoplasia grade 2 or higher (CIN2) of Alinity testing on FVU (ratio, 0.94; 95% CI, 0.85-1.03), mC (ratio, 1.00; 95% CI, 0.94-1.06), and EB/QT (ratio, 0.92; 95% CI, 0.85-1.00) was not different to CCSs. Specificity on FVU was similar to CCS (ratio, 1.02; 95% CI, 0.95-1.10), whereas specificity on mC was lower (ratio, 0.83; 95% CI, 0.76-0.90), but on EB/QT was higher (ratio, 1.08; 95% CI, 1.01-1.15) than on CCS. Accuracy on EB (sensitivity ratio, 0.96; 95% CI, 0.87-1.05; specificity ratio, 1.18; 95% CI, 1.06-1.31) was slightly better than on QT (sensitivity ratio, 0.88; 95% CI, 0.75-1.03; specificity ratio, 1.00; 95% CI, 0.92-1.09). In conclusion, clinical sensitivity of Alinity assay on all self-sample types was similar to cervical specimens. Adjustment of signal thresholds improved assay’s accuracy to detect CIN2 in all self-sample types.