Human papillomavirus (HPV)-associated anogenital cancers and their precursor lesions occur in excess in human immunodeficiency virus (HIV)-infected patients despite the initiation of highly active antiretroviral therapy. In this context, a drastically increased relative risk for anal intraepithelial neoplasia (AIN) exists in HIV-infected men having sex with men (MSM). In a pilot study, imiquimod, a topical immune response modifier, has been reported to be beneficial in the treatment of AIN. To investigate the role of several biomarkers as potential adjuncts in the course of imiquimod treatment for AIN, and to determine whether these markers correlate with the course of high-risk HPV DNA load during imiquimod therapy. Immunohistochemical staining was performed for p16(ink4a), minichromosome maintenance protein (MCM), Ki67, proliferating cell nuclear antigen (PCNA) and p21(waf1) expression before and after 16 weeks of imiquimod treatment for AIN. High-risk HPV DNA load determinations were performed by real-time polymerase chain reaction with type-specific primers and probes for HPV types 16, 18, 31 and 33. Histopathological and virological analyses were performed in 21 HIV-infected MSM with histologically confirmed AIN. Eighteen (86%) patients had a complete histological clearance of AIN after imiquimod therapy. As previously shown, lesional high-risk HPV DNA load significantly decreased during imiquimod therapy. Moreover, a significant decline of p16(ink4a), Ki67, MCM and PCNA expression after treatment was observed, while p21(waf1) expression changed nonsignificantly after imiquimod therapy. A significant correlation between the course of high-risk HPV DNA load and p16(ink4a) expression was observed during imiquimod treatment of AIN, whereas the decline of high-risk HPV DNA load did not significantly correlate with MCM, Ki67, PCNA or p21(waf1) expression. The significant decrease in p16(ink4a) expression in correlation with the drop of lesional high-risk HPV load suggests that p16(ink4a) may be a useful adjunct for the evaluation of treatment response in HPV-associated malignancies and their precursor lesions.