To resist the harsh intrinsic milieu, several lines of defense exist in the stomach. The aim of this study was to investigate the effect of the gastric pathogen Helicobacter pylori on these mechanisms in vivo. We used FVB/N mice expressing human -1,3/4-fucosyl transferase (producing Leb epitopes), inoculated with H.pylori 1. The mice were anesthetized with isoflurane or Hypnorm/midazolam and the stomach was exteriorized and the surface of the corpus mucosa exposed. Mucus thickness was measured with micropipettes, juxtamucosal pH (pH_jm) with pH-sensitive microelectrodes, blood flow with laser-Doppler flowmetry, and mRNA levels of the bicarbonate transporter SLC26A9 quantified with real time PCR. The increase in mucosal blood flow seen in response to luminal acid (pH 1.5) in control animals (140±9% of control) was abolished in infected mice. The firmly adherent mucus layer was significantly thinner in infected (31±2 µm) than in control mice (46±5 µm) and no mucus accumulation occurred in the infected mice. Juxtamucosal pH decreased significantly more on exposure to luminal acid in infected mice (luminal pH 1.5 pH_jm 2.4±0.7) than in control mice (pH_jm 6.4±0.5). In spite of a reduced pH_jm SLC26A9 mRNA expression was significantly increased 1.9-fold in infected mice. The reduction in pH_jm by infection with H.pylori might be due to a reduced firmly adherent mucus layer, increased mucus permeability to H⁺ and/or inhibition of bicarbonate transport. The upregulation of SLC26A9 in H.pylori infected epithelium might be a result of continuous inhibition of the transporter by e.g. ammonium, a H.pylori product, earlier shown to inhibit SLC26A9.