In order to predict the potential benefit of pneumococcal conjugate vaccines (PCV), we evaluated the serotype coverage of the 7-, 9-, 11- and 13-valent PCV over the isolates causing invasive pneumococcal disease (IPD) in Thai children. One hundred and fifteen Streptococcus pneumoniae isolates from sterile sites in children younger than 5 years old between 2000 and 2005 were serotyped. The coverages of 7-, 9-, 11-, and 13-valent PCV were 69%, 73.8%, 73.8% and 85.7% in children younger than 2 years, and 73.9%, 77.4%, 77.4% and 87.8% in children younger than 5 years of age, respectively. 69.6% and 22.6% of the isolates were non-susceptible to penicillin and cefotaxime. 7-valent PCV covered 89% and 100% of penicillin and cefotaxime non-susceptible isolates.