OBJECTIVES: Pneumococcus was responsible for more than 50% of the preventable deaths in infants under 5 years of age according to the Pan American Health Organization before the introduction of conjugate vaccines. The objective of this analysis is to evaluate the cost effectiveness of vaccinating the Bogota, Colombia population younger than 2 years of age with 13- valent vaccine (PCV 13) in comparison to the 10-valent or PHiD-CV vaccine (PCV 10) both in same schedule. METHODS: In order to estimate the costs and the impact of the pneumococcal disease, a Markov model simulating vaccination and outcomes of 10 annual birth cohorts was adapted to the Colombian conditions from the Health System perspective. The probabilities and the costs were extracted from a literature review and tariff manuals applicable for Colombia for January 2011, with costs presented in US$. The results in health are expressed as number of cases of diseases and deaths prevented, as well as in terms of life years saved (LYs). Probabilistic sensitivity analyses were done. RESULTS: Over a 10 year period, vaccinating with PCV13 prevents 1,680 cases of invasive pneumococcal disease, 9,842 hospitalized pneumonia, 805 non complicated pneumonia,  16,011 cases of acute Otitis media and 473 deaths, saving 11,414 LY’s compared to PCV10. The total costs including vaccination costs and medical costs are US$ 7,828,204 less for PCV13 compared to PCV10 (US$ 215,750,926 vs. US$ 223,579,130). The model shows robustness in the sensibility analysis. CONCLUSIONS: The analysis suggests that vaccinating infants with PCV13 in Bogotá, Colombia is a cost-saving alternative in comparison with PHiD-CV. The results in economic and disease burden are substantial and they support the decision making in favor of PCV13 for its high impact in public health.