Helicobacter pylori-infected gastric mucosa is characterized by high levels of interferon-γ (IFN-γ), but whether the high level of IFN-γ regulates the virulence of H. pylori is unclear. Here, we characterized the response of H. pylori to IFN-γ and found by indirect immunofluorescence that IFN-γ can bind to H. pylori. The binding resulted in the altered expression of 14 proteins, including the virulence factor, cytotoxin-associated gene A (CagA), whose expression was downregulated. The transcription and translation of CagA downregulated by IFN-γ was further confirmed by reverse transcriptase-PCR and Western blot analysis. We co-cultured the human gastric cancer cell line AGS with H. pylori exposed to IFN-γ; both phosphorylated CagA and nonphosphorylated CagA in AGS cells were downregulated by IFN-γ, and the proportion of cells with the 'hummingbird' phenotype was also decreased. Thus, IFN-γ can help control H. pylori infection indirectly through the virulence factor CagA.