Most guidelines currently recommend the testing of human papillomavirus (HPV) in ASCUS cases. The most used method for this purpose is Hybrid Capture II (HCII), but PCR techniques with GP5+/6+ primers can be also applied. Furthermore, the HCII high-risk probe test for detection of HPV shows cross-reactivity with low-risk HPV. Although this cross-reactivity has been studied in screening populations, it has received little attention in ASCUS cases. To compare the performance of the HCII high-risk probe test and PCR for the detection of HPV in ASCUS cases. We randomly selected 83 ASCUS cases that were positive for high-risk HPV by HCII and applied the PCR test using MYO9-11 and GP5+/6+ primers to samples from these cases. Our results show cross-reactivity with low-risk HPV in 25.3% (21/83) of the HCII+ PCR+ cases. Regarding the follow-up our results emphasize the importance of HPV typing, especially for HPV 16 infection. We propose the use of PCR techniques using GP5+/6+ consensus primers for the screening of HPV in ASCUS. Copyright © 2011 Wiley Periodicals, Inc.