OBJECTIVES: In 2011 PCV13 replaced PCV7 in Costa Rica’s National Immunization Program, however, continuation of the program is being evaluated based on considerations of cost-effectiveness. We evaluated the cost-effectiveness of continuing universal PCV13 infant vaccination versus limiting vaccination to high-risk children. METHODS: We used a decision-analytic Markov model to assess the impact of alternative pediatric PCV13 vaccination strategies: universal versus targeted to high-risk children only. For the universal strategy, outcomes are assessed for the entire Costa Rican population to capture indirect (herd) effects that accrue in the unvaccinated individuals. The model was populated using Costa Rican epidemiologic data and estimates from other published sources. Estimates of PCV13 effectiveness were extrapolated from observed PCV7 data, using assumptions regarding serotype prevalence and PCV13 protection against 6 additional serotypes.  Coverage was assumed to be the same for high-risk and the general population vaccination strategies. Outcome measures were incidence of invasive pneumococcal disease (IPD), pneumonia and acute otitis media (AOM); mortality, and net medical-care costs over 10 years from the societal perspective. RESULTS: Compared to no vaccination, the high-risk program would prevent 100 cases of IPD, 420 cases of hospitalized pneumonia (HP), 330 cases of non-hospitalized pneumonia (NHP), and 26,300 cases of AOM, and provide net savings of $460,000 over 10 years. Universal vaccination would prevent 2,200 cases of IPD, 14,800 cases of HP, 24,500 cases of NHP, and 367,000 cases of AOM for net savings of $34.8 million.  Compared to the high-risk program, universal vaccination would provide net savings of $34.3 million.  Excluding indirect effects, universal vaccination results in ICERs of $4,400 and $5,600 per QALY gained compared with no vaccination and high-risk vaccination, respectively CONCLUSIONS: Both high-risk and universal infant vaccination with PCV13 are cost-effective in Costa Rica; universal vaccination dominates both no vaccination and high risk vaccination due to indirect effects.