The Japan-specific sequence type (ST) clones, as well as several major epidemic-prone clones such as ST-32, have been identified previously among Neisseria meningitidis isolates in Japan. In this study, the infectious properties of various ST clones, including the two common Japan-specific ones, were examined and compared by in vitro infection assays using human endothelial and epithelial cell lines. The known invasive clones, as well as the Japan-specific ST-2032 strains that were frequently isolated from patients, exhibited high infectious abilities in adherence and invasion. In contrast, the Japan-specific ST-2046 and ST-198 strains, both of which were frequently isolated from carriers in Japan, were less efficient in adherence and invasion. The expression of the bacterial surface molecules such as pilin, Opc, Opa and PilC, and the lipooligosaccharide structure, did not differ between disease-associated and carrier-associated isolates. These results suggest that in vitro infection assays may discriminate between disease-associated (patient-dominant) and carrier-associated (carrier-dominant) meningococcal ST clones. The ST-2032 clone showed the highest infectious activity in vitro, suggesting that it may possess some unidentified factors necessary for the infectious ability that were not present in the ST-2046 clone with the lowest infectious ability.