OBJECTIVE: To estimate the prevalence, incidence, and clearance of abnormal vaginal cytology and vaginal intraepithelial neoplasia (VAIN) in human immunodeficiency virus (HIV)-seropositive women. METHODS: Pap tests were done semiannually for 335 HIV-seropositive and 75 HIV-seronegative women with prior hysterectomy in the prospective Women's Interagency HIV Study cohort. End points included abnormal Pap test results after hysterectomy and VAIN regardless of hysterectomy. RESULTS: Over a median of 5.6 years of follow-up, vaginal Pap test results were abnormal at 1,076 (29%; 95% confidence interval [CI] 25-33%) of 3,700 visits among HIV-seropositive compared with 31 (4%; 95% CI 2-8%) of 763 visits among HIV-seronegative women (P<.001). Abnormal Pap test results included 641 atypical squamous cells of undetermined significance, 425 low-grade squamous intraepithelial lesions, and 10 high-grade squamous intraepithelial lesions in HIV-seropositive women and 28 atypical squamous cells of undetermined significance and three low-grade squamous intraepithelial lesions in HIV-seronegative women. The incidence of abnormal Pap test results after hysterectomy was 14 per 100 person-years among HIV-seropositive and two per 100 person-years among HIV-seronegative women (P<.001) and remained stable across time. The 5-year clearance rate of abnormal Pap test results was 34 per 100 person-years for HIV-seropositive and 116 per 100 person-years for HIV-seronegative women (P<.001). In multivariate regression models, women with lower CD4 counts were more likely to have and less likely to clear abnormal cytology when it occurred. The incidence of VAIN 2 or worse was 0.2 and 0.01 per 100 person-years for HIV-seropositive and HIV-seronegative women (P=.001). Two HIV-seropositive women developed stage II cancers with remission after radiotherapy. CONCLUSION: Vaginal Pap test results are often abnormal in HIV-seropositive women. Although more common than in HIV-seronegative women, VAIN 2 or worse and especially vaginal cancers are infrequent.