OBJECTIVES: To estimate the costs of pneumococcal disease in Brazil, Chile and Uruguay, to describe how these costs vary between different patient groups, and to discuss factors that affect these cost variations. METHODS: The cost of pneumococcal disease was estimated from the health care perspective. For each country, baseline cost estimates were primarily developed using health resources information from patient-level data and facility-specific cost data. A regression model was constructed separately for four types of pneumococcal diseases. The skewness-kurtosis test and the Cook-Weisberg test were performed to test the normality of the residuals and the heteroscedasticity, respectively. RESULTS: The treatment of pneumococcal meningitis generated up to US$ 5 435 per child. The treatment costs of pneumococcal pneumonia were lower, ranging from US$ 372 per child to US$ 3 483 per child. Treatment of acute otitis media cost between US$ 20 per child and US$ 217 per child. The main source of treatment costs variations was level of service provided and country in which costs were incurred. However, the tendency of costs to change with these variables was not statistically significant at the 5% level for most pneumococcal disease models. CONCLUSIONS: Pneumococcal disease resulted in significant economic burden to selected health care systems in Latin America. The patterns of treatment cost of pneumococcal disease showed a great deal of variation.