Clinical tests for human papillomavirus (HPV) DNA require clinical validation before being offered for use by laboratories. To determine the clinical viability of a laboratory-developed test using the Invader HPV reagents (Third Wave Technologies, Madison, WI), a retrospective study was designed using 213 patient cervical cytologic samples. The results of the Invader assay were directly compared with the results obtained using the Hybrid Capture 2 High-Risk HPV assay (Digene, Gaithersburg, MD). The results of both assays were also compared with cytologic evaluation. In addition, clinical performance was evaluated using a standard-of-care approach in which colposcopically guided biopsies were done in cases where standard of care dictated, and the histologic features of the biopsy specimens were noted. The Invader-based test demonstrated a clinical sensitivity in atypical squamous cells of undetermined significance cases of 98% for cervical intraepithelial neoplasia (CIN) 2 or worse and 100% for CIN 3 or worse and a negative predictive value of 96.9% (confidence interval, 89.3%-99.6%) using data generated mostly from the use of an earlier version of reagents. These findings support the clinical and laboratory benefits of the Invader method.