The present invention relates to a method for treating a Helicobacter pylori (IP) infection and/or an associated disease in an individual, comprising administering to the individual a therapeutically effective amount of a pharmaceutical composition containing a short-chain fatty acid or a pharmaceutically acceptable salt thereof, alone or in combination with an anti-HP agent, and a pharmaceutically acceptable carrier, wherein the short-chain fatty acid has the formula: in which R.sub.1 and R.sub.2, independently, are C.sub.1-C.sub.8alkyl or H, R.sub.3 is aryl or heteroaryl, and n is 0, 1, 2, 3, 4, 5 or 6. The present invention also relates to a method for treatment of Helicobacter pylori (HP) infection or disease associated with HP infection by administering a therapeutically effective amount of an HDAC inhibitor or a pharmaceutically acceptable salt thereof, alone or in combination with an anti-HP agent, and a pharmaceutically acceptable carrier.