OBJECTIVES: Streptococcus pneumoniae is presumed to be the major etiology agent responsible for a significant amount of meningitis, bacteremia and sepsis (invasive pneumococcal disease; IPD) as well as Community Acquired Pneumonia (CAP) and Acute Otitis Media (AOM). The Czech Republic (CR), as well as many other European countries have only a limited local evidence on the underlying epidemiology. The objective was to estimate the expected outcomes, costs, cost-effectiveness of the pediatric national immunization program (NIP) with 13-valent pneumococcal conjugated vaccine (PCV13) and 10-valent pneumococcal conjugated vaccine (PCV10) as a comparator among specific populations of children and adults in preventing and reducing the incidence of IPD, CAP and AOM in CR. METHODS: A Markov decision-analytic model was developed to examine impacts of infant vaccination with PCV13 versus PCV10. PCV13 direct effectiveness was extrapolated from PCV7 efficacy data from clinical trials, using assumptions regarding serotype prevalence and PCV13 protection against additional serotypes, while indirect (herd) effect was extrapolated from US surveillance data following universal PCV7 use. The local epidemiology and cost data were used to achieve maximum national specificity. RESULTS: Model predicts incremental EUR 64.5 million for the PCV13 NIP from the payer’s perspective in the 10-year horizon, as compared to PCV10. This would lead to an reduction in IPD, all cause inpatient and outpatient CAP and AOM by approximately 921, 22 900, 56 796 and 40 598 cases, respectively, thus savings EUR 35.4 million. This gives a total cost of EUR 29.0 million in the 10 years. The incremental cost per LYG or QALY gained is estimated as EUR 929 or EUR 1 164, respectively, from the payer’s perspective as compared to PCV10. CONCLUSIONS: Comparing the national GDP per capita with the WHO recommendation on health care spending per QALY gained, PCV13 NIP in Czech Republic can be considered cost-effective.