The ability of Helicobacter pylori to activate neutrophils is associated with peptic ulcer disease (PUD). One of the H. pylori factors previously suggested to stimulate neutrophil activation is the H. pylori neutrophil-activating protein (HpNAP). The primary aims of this study were to investigate the relationships between H. pylori neutrophil activation and reported variations in HpNAP expression and the napA gene sequence. The association between neutrophil activation and vacuolating cytotoxin activity was also investigated. The ability to activate neutrophils was found here to be associated with the development of PUD and was a characteristic more frequently identified in H. pylori isolates with vacuolating cytotoxin activity. However, no relationship was found between neutrophil activation and the expression of HpNAP or differences in the napA sequence. In conclusion, the ability to activate neutrophils contributes to the ulcerative potential of individual H. pylori isolates, but this activity is not mediated by differences in HpNAP.