Helicobacter pylori is a flagellated chronic pathogen, which colonizes the gastric mucus and mucosal cell surfaces. Flagella and motility are essential for the survival of this bacterium in the stomach environment. Flagellins of several bacterial species are potent activators of the human innate immune system by binding to TOLL-like receptor 5 (TLR5). The possible role of the two H. pylori flagellins FlaA and FlaB in stimulation of the innate immune system and induction of IL-8 release by human gastric epithelial cells was investigated in this study. Transcription and expression of TLR5 in three different human gastric epithelial cell lines was demonstrated. Salmonella enterica serovar Typhimurium FliC flagellin was able to activate human gastric epithelial cells. TLR5 transcription was modulated by H. pylori infection. However, both H. pylori flagellins appeared to possess no immunostimulatory potential on human gastric cells via TLR5, despite their extensive amino acid homology to stimulating flagellins of other bacterial species. The evolutionary development of such unique flagellins of low activating potential is proposed to be a novel mechanism of H. pylori to preserve the essential function of its flagella during chronic colonization of the stomach and to evade the deleterious host immune responses.