The availability of new polysaccharide-protein conjugate vaccines against Neisseria meningitidis serogroup C prompted European National Health authorities to carefully monitor isolate characteristics. In Italy, during 1999-2001, the average incidence was 0.4 cases per 100,000 inhabitants. Serogroup B was predominant and accounted for 75% of the isolates, followed by serogroup C with 24%. Serogroup C was isolated almost twice as frequently in cases of septicemia than in cases of meningitis, and the most common phenotypes were C:2a:P1.5 and C:2b:P1.5. Among serogroup B meningococci, the trend of predominant phenotypes has changed from year to year, with a recent increase in the frequency of B:15:P1.4. Only a few meningococci had decreased susceptibility to penicillin, and, in the penA gene, all of these strains had exogenous DNA blocks deriving from the DNA of commensal Neisseria flavescens, Neisseria cinerea, and Neisseria perflava/sicca. Fluorescent amplified fragment-length polymorphism analysis revealed the nonclonal nature of the strains with decreased susceptibility to penicillin.