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Typhi from Indonesia are a notable exception, with circulating strains expressing diverse flagella antigens including H<jats:italic>j,<\/jats:italic>H<jats:italic>d<\/jats:italic>and H<jats:italic>z66<\/jats:italic>. Hypothesizing that<jats:italic>S<\/jats:italic>. Typhi flagella plays a key role during infection, we constructed an<jats:italic>S<\/jats:italic>. Typhi<jats:italic>fliC<\/jats:italic>mutant and otherwise isogenic<jats:italic>S<\/jats:italic>. Typhi strains expressing the H<jats:italic>j,<\/jats:italic>H<jats:italic>d<\/jats:italic>, H<jats:italic>z66<\/jats:italic>flagella antigens. Phenotyping revealed differences in flagellum structure, strain motility and immunogenicity, but not in the ability of flagellated isolates to induce TLR5 activity. Invasion assays using epithelial and macrophage cell lines revealed differences in the ability of these<jats:italic>S<\/jats:italic>. Typhi derivatives to invade cells or induce cellular restructuring in the form of ruffles. Notably, the H<jats:italic>j<\/jats:italic>variant induced substantial ruffles that were not fully dependent on the GTPases that contribute to this process. These data highlight important differences in the phenotypic properties of<jats:italic>S<\/jats:italic>. Typhi flagella variation and how they impact on the pathogenesis of<jats:italic>S<\/jats:italic>. 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