The changes in cervical cytology characterization agreed on by the Bethesda committee meeting in 2001 created a category of atypical findings that has caused some management confusion. By description, the characterization of cervical cytology as only atypical implies a less worrisome prognosis. However, more than 40% of high-grade (CIN II or III or cancer) will be discovered within this category. The development and Food and Drug Administration approval of the Hybrid Capture 2 (HC-2; Digene Corporation, Gaithersburg, MD) for detecting high-risk human papillomavirus (HR-HPV) subtypes and the subsequent level I evidence supporting use of this test in the triage of women with atypical cytology has revolutionized the management of this cytology. With this success has come numerous additional uses for HR-HPV testing in the treatment and follow-up of women with a variety of cytologic abnormalities. This article reviews the literature on uses of HR-HPV testing in this population, with reference to currently accepted guidelines.