OBJECTIVES: Substantial evidence on the increased incidence of HPV-associated malignancies is mounting as a result of on-going natural history studies on HPV infections as well as vaccination trials. Yet, there remains a paucity of results from longitudinal studies on the natural history of anal, penile, and oropharyngeal cancers. The objective of this paper is the synthesis of the totality of evidence on anal, penile, and oropharyngeal cancers for the purpose of parameterizing decision analytic modeling. Following the known natural history of cervical carcinogenesis, our goal is to estimate the rates of transition from HPV infection to precancer, the rate of precancer clearance, and the rate of progression of precancer to cancer. METHODS: We conducted a systematic review of the literature to identify all articles with longitudinal data on the natural history of anal, penile, and oropharyngeal cancers. Including those studies that report quantifiable evidence, we conduct a meta-analysis on the core parameters. The review was performed as per the methods recommended by the Cochrane Collaboration. RESULTS: Using PubMed, we identified 605 articles relevant to the anal site, 540 articles for the penile site, and 267 on the oropharyngeal site. However, systematic review resulted in only 9 studies, all of which pertained to anal precancer/cancer. Given the available data, we estimated the annual rates of precancer clearance and progression to be 11.4% (8.34%, 14.55%) and 2.18% (0.92%, 3.47%), respectively. CONCLUSIONS: Decision analytic models provide a framework for formulation of vaccination policies, incorporating all available evidence. This review summarizes the totality of evidence on HPV and these three cancers to inform health policy, specifically policies concerning male vaccination against papillomavirus (MVP).