Background: The heptavalent pneumococcal conjugate vaccine (PCV-7) was introduced in high risk children and into the private market in Costa Rica in 2004 (<5% annual birth cohort). The aim of this study was to compare the Streptococcus pneumoniae serotype (ST) distribution, antibiotic resistance patterns and potential coverage before and after partial introduction of PCV-7.  Methods: A comparison between the S. pneumoniae isolates obtained and serotyped from the middle ear fluid (MEF) of Costa Rican children with otitis media between years 1999 and 2003 (before PCV-7 usage) and those isolates obtained from 2004 to 2008. Results: A total of 145 and 218 MEF S. pneumoniae were serotyped between years 1999 and 2003 and 2004 and 2008, respectively. Considering a 19F outbreak observed between years 1999 and 2003, the following statistically significant changes in serotype distribution were detected between 1999 and 2003 and 2004 and 2008: ST 3: 4.8–12.8% (P = 0.01); ST 11A: 0–4.1% (P = 0.01); ST 14: 3.5–21.1% (P < 0.001) and ST 19F: 52.4–18.3% (P < 0.05). Comparison of the two study periods demonstrated that during 2004 and 2008 a statistically significant decrease in penicillin non-susceptible serotypes (36.2–20.4% [P = 0.003]) and a statistically significant increase in trimethoprim-sulfametoxazole resistant serotypes (54.9–68.5%, respectively [P = 0.03]) was observed. Potential pneumococcal vaccines coverage between 1999 and 2003 and between 2004 and 2008 were: for PCV-7: 77.2–60.5%, respectively (P = 0.001); for the 10-valent conjugated vaccine (PCV-10): 78.6–61.4%, respectively (P = 0.0008) and for the 13-valent conjugated vaccine (PCV-13): 84.8–79.3%, respectively (P = 0.2).  Conclusions: Changes in the serotype distribution and antimicrobial susceptibility of MEF S. pneumoniae have been observed in Costa Rican children with OM. Because of the limited use of PCV-7 during the study period, these changes probably cannot be attributed to PCV-7 use. Between 2004 and 2008, PCV-13 offered the highest potential vaccine coverage.