A case-control study compared detection by polymerase chain reaction (PCR) specific for human papillomavirus (HPV) type 16 with restriction enzyme analysis and Southern blot hybridization detection of HPV type 16. Cervicovaginal lavage samples from 64 women with histopathologic evidence of a cervical squamous intraepithelial lesion and 55 samples from cytologically healthy women were studied. Several methods of PCR product analysis, including radioactive and nonradioactive probing, were compared. The sensitivity of HPV detection by PCR when the amplified DNA fragment was visualized on a gel was equivalent to those of detection by restriction enzyme and Southern blot analyses. Hybridization of the PCR product with radioactively or nonradioactively labeled oligonucleotide probes increased the sensitivity of HPV detection by 100-fold. However, an increase in the sensitivity of the assay preferentially identified low levels of the virus in cytologically healthy women. Therefore, the value of HPV detection in identifying women with cervical neoplastic disease was greater, and the odds ratio for the presence of a cervical squamous intraepithelial lesion was higher when the less sensitive modalities were used. These results suggest that quantitation of HPV by PCR may maximize the clinical significance of a positive test result. Further studies will be needed to determine the optimal level of virus detection which has the highest positive predictive value of clinical disease.