Background & Aims: The growth of gastric mucosa-associated lymphoid tissue lymphoma (MALToma) seems to depend on the stimulation of Helicobacter pylori. We attempted to identify specific antigen(s) from ii. pylori strains associated with MALToma. Methods: Membranous and secreted proteins of ii. pylori were compared on sodium dodecyl sulfate-polyacrylamide gel electrophoresis by Western blot using sera from patients with MALToma. Results: A 19-kilodalton protein was seen in all strains isolated from patients with MALToma but uncommonly in other strains. The protein was purified and sequenced. Amino acid sequence comparison showed it was an FldA homologue, a putative flavodoxin protein. DNA sequencing in 26 strains revealed that a nucleotide G insertion at position 481 of the fldA gene was move frequently observed in strains associated with MALToma than other strains (9/9 vs. 6/17; P = 0.002). The mutation caused a short truncation. A recombinant protein with this truncation was expressed and tested. Sera of 12 (70.6%) of 17 patients with MALToma were positive for the antibody to the recombinant protein, and 7 (16.7%) of 42 control patients were positive (12/17 vs. 7/42; P < 0.0001). Conclusions: Truncated FldA of H, pylori is associated with gastric MALToma. It may be involved in the pathogenesis of gastric MALToma. Antibody to this antigen could be used as a serological marker of the disease.