Objective: To describe the natural history of genital warts and vulvar intraepithelial neoplasia (VIN) in women with human immunodeficiency virus (HIV). Methods: A cohort of 2,791 HIV-infected and 953 uninfected women followed for up to 13 years had genital examinations at 6-month intervals with biopsy for lesions suspicious for VIN. Results: The prevalence of warts was 4.4% (5.3% for HIV-seropositive women and 1.9% for HIV-seronegative women, P<.001). The cumulative incidence of warts was 33% (95% confidence interval [CI] 30-36%) in HIV-seropositive and 9% (95% CI 6-12%) in HIV-seronegative women (P<.001). In multivariable analysis, lower CD4 lymphocyte count, younger age, and current smoking were strongly associated with risk for incident warts. Among 501 HIV-seropositive and 43 HIV-seronegative women, warts regressed in 410 (82%) seropositive and 41 (95%) seronegative women (P=.02), most in the first year after diagnosis. In multivariable analysis, regression was negatively associated with HIV status and lower CD4 count as well as older age. Incident VIN of any grade occurred more frequently among HIV-seropositive than HIV-seronegative women: 0.42 (0.33-0.53) compared with 0.07 (0.02-0.18) per 100 person-years (P<.001). Positivity for VIN 2 was found in 58 women (55 with and three without HIV, P<.001). Two women with HIV developed stage IB squamous cell vulvar cancers. Conclusion: Although genital warts and VIN are more common among HIV-seropositive than HIV-seronegative women, wart regression is common even in women with HIV, and cancers are infrequent.