OBJECTIVES: Two human papillomavirus (HPV) vaccines currently exist: a bivalent targeting oncogenic high-risk HPV-16/18 and a quadrivalent targeting high-risk HPV-16/18 and low-risk HPV-6/11. Based on data in their respective trials, the bivalent vaccine is likely to have higher efficacy against non-vaccine oncogenic HPV-types (cross protection). The quadrivalent has an additional effect against genital warts. The differences in the annual impact of both vaccines on precancerous lesions, genital warts (GW) and cervical cancer (CC) were evaluated. METHODS: A static prevalence-based model was developed, which estimates the differences in lesions, GW, CC, and costs prevented between the two vaccines over a one-year period at steady state (i.e. when all women are vaccinated). The base case analysis was performed from a health care payer’s perspective, including only National Health Insurance covered costs.  In addition, an analysis from a societal perspective was performed, including also indirect costs and out-of-pocket payments.  Epidemiological and cost data were obtained from published sources. Efficacy figures were based on the latest results from each vaccine’s respective clinical trial. Univariate sensitivity analyses were conducted, in which parameters were varied 20% up and down from the baseline value. RESULTS:  Under this model, the bivalent vaccine would result in an additional reduction of 1,486 ASCUS; 1,768 CIN1; 1,230 CIN2/3 and 166 CC cases per year, while the quadrivalent vaccine would result in an additional 7,726 GW cases prevented per year. The additional annual costs averted with the bivalent vaccine was estimated at US$ 1.3 million and US$ 1.9 million from a health care payer’s and societal perspective, respectively. This outcome is most sensitive to cross protection figures. CONCLUSIONS:  Vaccination with the bivalent vaccine is expected to have a higher impact than the quadrivalent vaccine on the prevention of precancerous lesions and CC in Taiwan, and would lead to more cost averted.