For many years, invasive meningococcal disease in the Czech Republic occurred sporadically and was caused mainly by meningococci of serogroup B. In 1993, when a new clone (ET-15/37) emerged, the only phenotype found was C:2a:P1.2,5. In 1995, an antigenic variation of the ET-15/37 clone, B:2a:P1.2,5, occurred. The results of immunological surveys conducted in 1989 and 1996 were compared. A significantly higher proportion of 1996 sera than those collected in 1989 showed bactericidal antibodies against N. meningitidis B:2a:P1.2,5 (19.7 vs. 5.1%) and N. meningitidis C:2a:P1.2,5 (15.9 vs. 7.4%), consistent with increased herd immunity due to the spread of the new clone in the Czech Republic. There were differences in the age distribution of the positive sera.