PorA protein is an important component of group B meningococcal protein-based vaccines. The goals of this study were: (i) to classify the non-serosubtypable strains recovered from vaccine failures and controls by porA variable region (VR) type; (ii) to investigate if point mutations of VRs of the porA gene are present in P1.19,15 strains recovered from vaccine failures and controls; (iii) to investigate if nucleotide sequence variation in the promoter region of porA gene is related to low expression of PorA protein. VR type P1.19,15 predominated in younger vaccine failures (3-47 months) compared to older failures (48-83 months). No changes in VRs of porA were observed in 46 P1.19,15 strains studied. A promoter spacer of 16bp and 10 guanidine residues in the polymeric G tract was detected in five of six strains with weak PorA expression. Overall, this study indicated that lack of antibody response was probably the major cause of low vaccine efficacy in young children.