OBJECTIVES: Estimate the costs averted and cases prevented of genital warts of the quadrivalent HPV6/11/16/18 vaccination program in a two-dose scheme in girls of 9-11 years old compared to an HPV 16/18 vaccination program in Ecuador, while preventing effectively for cervical cancer with both vaccines. METHODS: A previously developed transmission dynamic mathematical model (Elbasha & Dasbach, 2010) was adapted to evaluate the impact of routine vaccination of 9-11 year-old females. The model assumed coverage of 90% for two doses of HPV6/11/16/18 vaccine at international price rates versus HPV16/18 vaccine.  Ecuador’s model cost input data was estimated (Roldos & Bustamante 2014); and Ecuador´s disease values when available and Latin American values otherwise .  RESULTS: In a 100-year period , HPV6/11/16/18 vaccination would result in reductions of HPV 6/11-related disease incidence at the population level as follows: genital warts in females (81.7%), genital warts in males (78.6%) and HPV6/11-related CIN1 (79.7%) . These results would translate into a reduction of HPV 6/11-related disease cost of between 55% to 60% for genital warts among females, genital warts among males, and HPV6/11-related CIN1, respectively.  Under the model assumptions, the estimated net cost of vaccination with the HPV6/11/16/18 vaccine from a public health perspective would be close to -USD$190 million, adjusted to the net present value, this cost-saving represents USD$180,735,849.09 with a present value interest factor of 0.9512.  CONCLUSIONS: In Ecuador, routine vaccination of 9-11 year old females with a quadrivalent HPV6/11/16/18 vaccine is cost-saving compared to a bivalent HPV 16/18 vaccine, which suggests a significant public health and economic impact.