A total of 522 Streptococcus pneumoniae invasive isolates from diverse sources were collected from January 2002 to December 2003 in Taiwan in order to understand the serotype distribution of invasive isolates in Taiwan. The most frequently isolated serotypes of S. pneumoniae were types 14 (18.4 %), 23F (15.1 %), 3 (13.8 %), 19F (13.4 %), 6B (8.2 %), 9V (3.6 %) and 4 (2.5 %). The majority of cases were either under 5 years of age (24.1 %) or older than 65 years (36.6 %). Serotype distribution in adults aged over 14 years and children aged under 2 years was similar, except for that of type 3, which was more prevalent in adults. Penicillin-non-susceptible strains accounted for 67.7 % of all strains and were the predominant strains of serotypes 23F, 19F, 6B and 14. Most strains were susceptible to cephem drug, 85.7 % of isolates were susceptible to cefotaxime and 92.9 % were susceptible to ceftriaxone. A total of 72.6 % (379/522) of the isolates were resistant to at least two antibiotics. The 23-valent vaccine in the current commercial market would cover 87.2 % of the serotypes and 100 % of the penicillin-non-susceptible serotypes of S. pneumoniae in Taiwan. The coverage of 7- and 11-valent protein conjugate vaccines of the serotypes in children under 2 years of age would be 78.8 and 86.5 %, respectively. These results will help to assess the adequacy of the vaccine formulations marketed in Taiwan.