Reproducible induction of sterilizing immunity, essential for an effective Helicobacter pylori vaccine, remains elusive. As motility is essential for gastric colonization by Helicobacter, we evaluated whether a vaccine targeting flagella induces improved protection. Mice immunized with a vaccine enriched for H. pylori flagella sheath proteins exhibited significantly reduced colonization, equivalent to that observed in mice immunized with whole-cell lysate. Two-dimensional profiles indicated that flagella contain proteins not evident in whole-cell lysate. Moreover, comparison of Western blot profiles using whole-cell lysate antisera revealed striking differences in antigenicity.