We conducted a study to examine the clonal distribution of invasive serotype 1 and 5 isolates as representatives of serotypes that are rarely carried by healthy individuals compared to that of invasive serotype 6B and 23F isolates as representatives of serotypes often carried by young children for prolonged periods. All invasive serotype 1, 5, 6B, and 23F isolates recovered from blood cultures during January 1995 to May 1999 were analyzed; these included 66 serotype 1, 30 serotype 5, 11 serotype 6B, and 15 serotype 23F isolates. One hundred thirty-three nasopharyngeal (NP) isolates of the indicated four serotypes from healthy children were also studied. The strains were characterized using serotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis profiling. We found that both invasive and NP serotype 1 and 5 isolates were susceptible to penicillin and that each serotype showed only one clonal type. In contrast, serotype 6B and 23F strains showed different phenotypic characteristics as well as multiple clonal types; 10 clones were identified among 6B isolates, and 11 clones were identified among 23F isolates.