The in vitro effect of ammonium bicarbonate buffer on mucus H+ permeability is reported here. The diffusional resistance of mucus and water was demonstrated to be dependent on buffer concentration, and the contrast between the two types of layers was most pronounced for low buffer concentration near neutrality. Moreover, the pKa values of HCO3- and NH3 had a profound effect on measured DHCl. These in vitro studies suggest that a potentially damaging high local concentration of NH3 and HCO3- within the mucus layer generated by the action of Helicobacter pylori urease on endogenous intragastric urea could greatly accelerate proton flux to the surface epithelium by operation of a buffer shuttle. This results in enhanced H+ permeability, particularly at pKa values of HCO3- and NH3, and that in extreme circumstances this may result in gastric ulcer formation.