Background: A vaccine has recently been licensed in many countries that protects against the human papillomavirus types 6, 11, 16, and 18. Types 6 and 11 account for approximately 90% of anogenital warts (AGWs). We describe the 20-year trends in the incidence and prevalence of AGWs in Manitoba, Canada. Methods: We used linked population-based hospital and physician databases for Manitoba for 1984 to 2004. Cases were identified using tariff (billing) and ICD codes. A case was considered to be incident if it was preceded by a 12-month interval free period of AGWs care. Otherwise, it was deemed to be prevalent. An episode was considered over once a 12-month interval had elapsed without an AGW claim. Results: Approximately 25,000 Manitobans were diagnosed with AGWs between 1985 and 2004. The annual age-standardized incidence rates peaked in 1992 (men, 149.9/100,000; women 170.8/100,000). In recent years, the rates have been increasing again, particularly for men. The male:female incidence rate ratio increased from 0.76 in 1985 to 1.25 in 2004. The highest incidence rate tended to be in those aged 20 to 24 years. Trends in prevalence were similar. Prevalence in 2004 was 165.2/100,000 for men and 128.4/100,000 for women. Conclusions: These population-based findings suggest that AGWs are a substantial burden to Manitobans and that their pattern has changed over time, with incidence and prevalence becoming higher in men than women. Monitoring the future trends in AGWs will provide an early marker of the effectiveness and duration of protection of human papillomavirus vaccination at a population level.