The percentage of Neisseria meningitidis serogroup Y isolated from patients with invasive meningococcal disease (IMD) in Italy has increased from 1998 to 2006. In this study, phenotypic features and genetic relatedness have been investigated in all serogroup Y meningococci isolated during that period. Multilocus sequence typing (MLST) identified the ST-23 complex/Cluster A3 as the major clonal complex in 88.8% of the strains. That complex included all strains belonging to the sequence type (ST) 23 isolated from 1998 to 2004, whereas the ST-3171 was prevalent among strains in the years 2005 and 2006. The STs 23 and 3171 differ for only one nucleotide in the phosphoglucomutase (pgm) housekeeping gene. Over 80% of serogroup Y ST-23 complex/Cluster A3 strains showed phenotype Y:14:NST and 85% of the latter resulted indistinguishable by pulsed-field gel electrophoresis analysis. In 2005, serogroup Y meningococci with decreased susceptibility to penicillin were isolated for the first time in Italy. In the following year, three of the seven strains showed this phenotype. The results of this study allow us to draw a profile of the molecular characteristics of invasive serogroup Y in Italy and will be helpful to monitor the spread of this serogroup in the next years.