Studies from the era prior to the introduction of highly active antiretroviral therapy (HAART) have shown that the prevalence of anal human papillomavirus (HPV) infection and anal squamous intraepithelial lesions (ASIL) was very high among human immunodeficiency virus (HIV)-positive homosexual men, and to a lesser extent, among HIV-negative homosexual men. Prospective data also show that the incidence of high-grade ASIL (HSIL), the putative invasive cancer precursor lesion, was high among both HIV-positive and HIV-negative men. Studies of HIV-positive women and HIV-negative women at high risk of HIV show a high prevalence of anal HPV infection and ASIL. Early data suggest that most anal HSIL lesions do not regress after an individual begins HAART. Since progression of anal HSIL to invasive anal cancer may require several years, the improvement in survival associated with HAART may paradoxically lead to an increased risk of anal cancer. Consistent with this, the incidence of invasive anal cancer has been increasing over the last few years among HIV-positive gay men, and is now approximately twice that of HIV-negative gay men. The potential to prevent anal cancer through detection and treatment of anal HSIL suggests a need to screen high-risk individuals with anal cytology, similar to the longstanding cervical cytology screening program currently used to prevent cervical cancer. Cost-effectiveness analyses indicate that anal screening programs should be cost-effective in HIV-positive men. However, barriers to implementation of screening preclude near-term implementation of such a program. These include an inadequate number of clinicians skilled in diagnosis and treatment of HSIL and lack of effective medical alternatives to surgical excision. Efforts are underway to address these issues and to better understand the natural history of ASIL in the HAART era.