Anal cancer may be prevented by treating anal high-grade squamous intraepithelial lesions (HSIL). Ablative therapies are the most commonly used treatments, but they may not be appropriate for all patients including those with extensive HSIL or bleeding diastheses. Researchers have studied topical therapies for human papillomavirus related lesions including anal HSIL. These therapies include patient-applied 5-fluorouracil, imiquimod and cidofovir, and provider-applied trichloroacetic acid. This review will discuss literature supporting efficacy of these products, which is based mainly on case series with few controlled trials having been conducted. Side effects are common with patient-applied topical therapy often requiring dose reduction and medication to treat pain. However, treatment discontinuations are infrequent. This review will also discuss some approaches to the use of these products in clinical practice.