OBJECTIVES Cervical cancer (CC) and genital warts (GW) are diseases associated with HPV infections. Two vaccines have been developed for the prevention of HPV infections. A quadrivalent vaccine which contains HPV types 6, 11, 16 and 18 and prevents both cervical cancer and genital warts and a bivalent vaccine (HPV types 16 and 18) which prevents only cervical cancer. The aim of this study was to determine public preferences for the two different vaccine characteristics and frequency of testing for Pap screening. METHODS Participants from across Canada completed the choice-based questionnaire for the following attributes: risk of cervical cancer and genital warts, frequency of Pap smear testing, need for a booster dose, target group (girls only or girls and boys), frequency of side effects and cost. Conditional logistic regression was used to determine the relative preferences and the willingness-to-pay (WTP) for each component in the vaccination strategy. RESULTS Of the 328 respondents, 51% were between the ages of 36-55 years, 58% were females, 46% had children, and 29% had some community college. With respect to HPV vaccination, 86% had fully vaccinated their children and 68% were considering the HPV vaccine. Respondents had a strong preference for a vaccine which provided protection against GW. Respondents also had a preference to avoid a yearly Pap smear and most preferred testing every 3 years. Respondents preferred lifetime protection from HPV vaccine and thus valued a booster dose every 10 years for their children. To reduce the risk of CC and GW by 1%, respondents had a WTP of $39 and $36, respectively for the vaccine. Respondents also preferred to vaccinate both boys and girls at a WTP of $23. CONCLUSIONS An HPV vaccine which provides protection against both CC and GW, and vaccinating both boys and girls appeared to be strongly associated with respondent preferences.