The genetic diversity of Streptococcus pneumoniae isolates (n=291) recovered from cerebrospinal fluid of patients with meningitis in France was investigated by restriction fragment length polymorphism analysis of the ribosomal RNA gene regions and of the pbp2b and 2x genes. Statistical analysis of the data by factorial analysis of correspondence established the following: penicillin-susceptible isolates had a high level of genetic diversity, especially those belonging to serogroups frequently associated with carriage; capsular serotype switches could occur among penicillin-susceptible and -resistant isolates; and the mechanisms of acquired penicillin resistance were clearly distinct in isolates with penicillin minimum inhibitory concentration (MIC) values <1 mg/L and isolates with penicillin MIC values >/=1 mg/L. Thus, an increase in the penicillin MIC for a given strain, from intermediate to high-level resistance would be a rare event.