With the aim of studying the molecular diversity of the antigens of a new recombinant vaccine against meningococcus serogroup B, the three genes coding for the main vaccine components GNA (Genome-derived Neisseria Antigen) 1870 (fHbp, factor H Binding Protein), GNA1994 (NadA, Neisseria adhesin A) and GNA2132 were sequenced in a panel of 85 strains collected worldwide and selected as representative of the serogroup B meningococcal diversity. No correlations were found between vaccine antigen variability and serogroup, geographic area and year of isolation. Although a relevant clustering was found with MLST clonal complexes, each showing an almost specific antigen variant repertoire, the prediction of the antigen assortment was not possible on the basis of MLST alone. Therefore, classification of meningococcus on the basis of MLST only is not sufficient to predict vaccine antigens diversity. Sequencing each gene in the different strains will be important to evaluate antigen conservation and assortment and to allow a future prediction of potential vaccine coverage.