Abstract Infection with the bacterium Helicobacter pylori is associated with both the development of gastritis and an attenuation in the hydrophobic properties of the stomach. In order to better understand the effect of ammonium, one of the major products of H. pylori urease on these properties, a series of in vivo and in vitro experiments was performed. In the in vivo studies rats were intragastrically administered NH4Cl alone and in combination with the mucolytic agent, Muco‐Mist, in various dosing strategies and concentrations. It was determined that the intragastric administration of four consecutive doses of a NH4Cl/Muco‐Mist mixture (20 mmol/L/5%) was capable of converting the stomach from a hydrophobic to hydrophilic state as determined by contact angle analysis. Further, the treated rats became more susceptible to the injurious effect of luminal acid as determined by measuring the haemoglobin concentration of a collected gastric perfusate. In the in vitro studies it was determined that exposure of the hydrophobic surface of a synthetic mucus gel layer to increasing concentrations of NH4Cl (0–20 mmol/L) resulted in a rapid transition to a hydrophilic state and an associated increase in the flux of H+ across its surface.Helicobacter pylori may induce an attenuation in both mucosal hydrophobicity and barrier properties by producing high concentrations of NH+4 in the mucus gel layer. The molecular mechanism of this action may be related to the chemical similarities of NH+4 and choline‐based phospholipids which contribute to the stomach's hydophobic surface.