Human papillomavirus (HPV) detection is an objective quality assurance benchmark for cervical cytology. There is no comparable metric for cervical biopsies despite biopsies having similar interobserver variability. Because HPV-16 positivity increases with the severity of cervical abnormality, we explored whether HPV-16 detection might be a useful metric for distinguishing a diagnosis of less than cervical intraepithelial neoplasia (CIN) 2 from CIN 2 or worse (representing the clinical threshold for treatment). By using Atypical Squamous Cells of Undetermined Significance-Low-Grade Squamous Intraepithelial Lesion Triage Study data, we compared biopsy diagnoses of the 10 clinical center (CC) pathologists with the quality control (QC) group. Although the percentage of HPV-16 correlated with severity of diagnoses, there was great variability between the rates for each individual CC pathologist. Agreement between individual CC pathologists and the QC group on the percentage of CIN 2 or worse containing HPV-16 correlated weakly with agreement on whether the diagnosis was less than CIN 2 or CIN 2 or worse. Thus the HPV-16 fraction was not found to be broadly useful as a quality assurance metric for biopsy diagnosis in this analysis.