Research has found that the majority of peptic ulcers are caused by an infection with a bacterium called Helicobacter pylori (H. pylori), and standard treatment in these cases is a combination of a proton pump inhibitor and the antibiotics amoxicillin and clarithromycin for two weeks. This is sometimes given in a single prescription called "Prevpac." In penicillin allergic people, a drug called metronidazole is sometimes substituted for the amoxicillin. Sometimes a PPI may be combined with bismuth (Pepto Bismol) along with the two antibiotics. After H. Pylori is eradicated, all of the antacid medications can be continued.

The effectiveness and side effects or risks associated with medical and surgical therapy for gastric disordershave been well studied. Newer endoscopic treatments are not yet as well studied. Some individuals who are helped by pharmacologic (drug) therapy, but who require long-term therapy, would prefer a non-surgical, non-pharmacologic option for treatment of their symptoms. This has led to research and development of newer endoscopic procedures designed to treat GERD. However, the safety and effectiveness of these procedures is yet to be established. Data has not yet established efficacy, safety, cost, durability and, possibly, reversibility; there is presently no definite indication for endoscopic therapy of GERD. Before undergoing any endoscopic antireflux procedure careful consideration of the alternatives should be talked about with a physician to gain a clear understanding of known side-effects, the absence of long-term data, and the risk of major complications.

Promotility drugs can be helpful in some people (after careful screening for known risk factors) with non-erosive GERD or mild esophagitis. Significantly, there are reported adverse effects of the drug cisapride (Propulsid) in people with certain preexisting conditions and some known drug interactions that can be associated with dangerous cardiac arrhythmias.