OBJECTIVES: No country in Asia-Pacific has yet introduced guidelines to differentiate between interventions with long-term and short-term impacts, unlike UK NICE who have recommended a lower rate (1.5%) be applied in the case of longer term benefits. HPV vaccines prevent against two diseases occurring at widely different time points: cervical cancer (CC) and genital warts (GW). This research aimed to explore the impact of discount rates (DR) on cost effectiveness outcomes associated with the comparative assessment of the two currently available HPV vaccines in Asia-Pacific. METHODS: A published Markov cohort model was adapted to assess the lifetime cost and benefits associated with the protection against CC and GW in Korea, Malaysia, Taiwan and the Philippines. DR of 1.5%, 3%, 5% were applied to each analysis. Vaccines are differentiated in their effectiveness against cervical cancer related disease (CC) and genital warts protection (GW). Cohort size was 253,000/986,910/153,000/259,000 for Korea/ Philippines/ Taiwan/ Malaysia, respectively. RESULTS: For KR, a DR of 5% and 3% resulted in a QALY difference between the two vaccines of -4 and +177, respectively. This was associated with the greater impact of the DR on CC outcomes (long-term) than GW (short-term). QALY benefit with CC increased dramatically with lower DR: 256/709/1,453 for Philippines, 129/353/768 for Taiwan and 91/253/510 for Malaysia by applying 5%/3%/1.5% DR, respectively. CONCLUSIONS: Selection of most appropriate vaccine can be reversed by the choice of DR in certain jurisdictions.  This can depend on model inputs relating to early benefits as DR increases emphasis on early benefits (GW) vs. late benefits (CC) for HPV Vaccination.  Policy makers in Asia-Pacific region should be mindful of the impact of the DR in HE analyses when making decisions.  This is especially the case for HPV vaccination whereby the primary objective (CC) is impacted more by a high DR relative to GW.