Streptococcus pneumoniae is a major cause of invasive infections. The aim of this study was to evaluate the serotype and antimicrobial susceptibility of invasive pneumococci isolated at 14 different centers in Turkey between January 2011–April 2012. Totally 79 clinical isolates from invasive infections were investigated, which were isolated from cerebrospinal fluid (CSF) (33, 42%), blood (31, 39%) and the other sterile body fluids (15, 19%). Susceptibility to penicillin, cefotaxime and erythromycin was determined by E-test (bioMerieux, France) according to CLSI standards. Latex agglutination method was used for determination of serogroups. Serotypes were determined by the capsular swelling (Quellung reaction) method (Denmark, Statens Serum Institute). It was found that most common serotypes among 79 strains were 19 F (12, 15%), 6 A (7, 9%), 23 F (5, 6%), 6 B (4, 5%), 19 A (4, 5%) and 3 (4, 5%). For all invasive pneumococcal diseases, during the first 2 years of age, the potential coverage rates of PCV7, PCV10, and PCV13 were 47.8%, 56.5%, and 82.6%, respectively; meanwhile 40.5%, 44.3%, and 63.3% for the pediatrics age group (0–18). Serotypes 19F, 6A, 19A, 23F, 6B, 14 and 3 were predominate. All pneumococcal conjugate vaccine formulations cover these serotypes with the exception of serotype 19A which is covered only by PCV13. Serotype 19A has steadily increased in prevalence and become increasingly resistant to common antibiotic classes. Rational antibiotic use and vaccination of infants with pneumococcal conjugate vaccines should be considered as essential strategies for prevention of pediatric invasive infections in Turkey.