Neisseria meningitidis capsular switching has been reported in several countries. In order to establish the genetic relationship within group B and C strains expressing subtypes 2a or 2b, and to evaluate whether C to B capsular switching occurred in Portugal, 64 meningococci (56 serogroup C and 8 serogroup B) isolated from invasive meningococcal disease were typed using molecular methods. The studied phenotypes, 2b:P1.5,2 and 2a:P1.5-1,10-8, were the most frequent among serogroup C, but were uncommon among serogroup B strains. The multi-locus sequence typing (MLST) allelic profile and the pulsed-field gel electrophoresis (PFGE) fingerprints showed that seven serogroup B strains were genotypically identical to C strains, suggesting that capsular switching occurred. Active laboratory surveillance to find evidence of capsule switching is a now priority as MenC was introduced in the Portuguese vaccination schedule in January 2006. [ABSTRACT FROM AUTHOR]