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Background: Anogenital warts (AGW) are caused by the most common sexually transmitted infection, human papillomavirus. The objective of this study was to examine AGW incidence from 1990 to 2011 by sex, age, income quintile, and residential area category (urban/rural). The study period included the initiation of school-based HPV vaccination for girls in the sixth grade, which began in 2008. The data presented in this paper may also be useful for establishing baseline rates of AGW incidence which may be used to evaluate the success of the school-based HPV immunization program.Methods: Cases of anogenital warts were identified using Manitoba's administrative databases of Physician Claims and Hospital Discharge Abstracts. Annual age-standardized incidence in Manitoba from 1990 to 2011 was calculated. Incident AGW rates were compared by sex, age group, residential area category (urban/rural), and household income quintile using logistic regression. Joinpoint regression analyses were used to evaluate the time trends of AGW.Results: Prior to 2000, AGW incidence was higher among females than males. However, from 2000 to 2011 the incidence was higher among males and increased steadily over time. AGW incidence tended to peak in younger age groups among females compared to males. Females and males living in urban areas had nearly twice the odds of AGW occurrence compared to those in rural areas.Conclusions: There is a need for education about AGW in male population. The upcoming initiation of HPV vaccination among boys may reduce the incidence and should be evaluated. [ABSTRACT FROM AUTHOR]