To determine the effect of highly active antiretroviral therapy (HAART) on high-risk human papillomavirus (HR-HPV) infections and related cervical lesions, the virologic and cytologic markers of HPV infection were prospectively studied in 163 human immunodeficiency virus (HIV)-infected women, including 27 untreated, 62 treated with reverse transcriptase inhibitors, and 74 treated with HAART. A high prevalence of both infections with HR-HPV types (68%) and squamous intraepithelial lesions (SILs; low grade, 20.2%; high grade, 6.2%) was observed. The risks of infection and disease were inversely correlated with CD4 cell counts (P=.015 and P=.022, respectively). During the observation period (mean, 15.4 months; range, 6-24 months), CD4 cell counts increased significantly only in subjects receiving HAART (P<.001). Persistence of HR-HPV infection and progression of SILs were comparable in the 3 groups. These results indicate that, even in the era of HAART, HIV-infected women should be monitored carefully for the emergence of high-grade SILs and cervical cancer.