Objective To investigate the impact of the fliD gene on the biofilm formation of Helicobacter pylori (H. pylori). Methods H. pylori fliD mutant was constructed using inverse PCR mutagenesis. The mobility of the bacteria and its adhesion ability to human epithelial cells were assessed using a motility assay and a fluorescein isothiocyanate staining adhesion assay, respectively. The formation of biofilm was evaluated using a pellicle assay and a crystal violet staining assay. The cyto-architecture of the biofilm was documented with scanning electron microscopy. Results It was found that there was no significant difference in the levels of bacterial adhesion and the biofilm formation between the wild-type ATCC 43504 and the fliD mutant. Apart from a poor motility, the fliD mutant had a slightly delayed formation of its biofilm and an incomplete cyto-architecture of its biofilm. The bacterial cells residing in the biofilm of the fliD mutant showed a loose accumulation with less apparent cross-linking fibrils. Most of the mutant cells had truncated flagella. Conclusions This study provides the preliminary evidences that fliD potentially regulates biofilm formation and is required for the motility of H. pylori. Further studies need to be performed in order to develop fliD as a novel target for vaccine or antimicrobial agent in future.