Helicobacter pylori induces chronic active gastritis that may progress to atrophy. Serious clinical consequences are peptic ulcer disease and gastric malignancies. Today, treatment of the infection is an appropriate option and is strongly recommended in various clinical situations. Although many antibiotics are effective against H. pylori in vitro, few substances are suitable for use in vivo. This is because H. pylori lives in a unique environment in which several factors may affect the pharmacokinetic and pharmacodynamic properties of the anti-microbial agents. One of the most important factors is gastric acidity. This article reviews the effects of acid suppression on H. pylori and the associated gastritis, the potential mechanisms by which anti-secretory drugs such as proton pump inhibitors might enhance the activity of anti-microbials in vivo, and the results of clinical trials supporting the current view that proton pump inhibitors are a mainstay in the treatment of this infection.