For some patients with severe reflux disease, an operation is an alternative option to long term use of medication. This applies especially to patients with resistant (at least 6 to 12 months) or complicated reflux esophagitis (with strictures) that does not respond fully to medical therapy or to patients in whom long term medical therapy is not desirable.

Usually a laparascopic fundoplication (in which the gastric fundus is wrapped around the esophagus so as to mimic a normal lower esophageal sphincter and prevent reflux) is performed. The laparoscopic (inserting a laparoscope through a tiny incision in the belly) approach has substantially reduced postoperative discomfort in comparison with open thoracotomy (opening the chest to perform surgery) or laparotomy (opening the abdomen ). The typical hospital stay at expert centers such as Johns Hopkins is only 1 to 2 days.

Antireflux therapy is effective in controlling the reflux symptoms. However, it does not usually result in reduction in length or grade of Barrett's esophagus. There is still a small risk of developing esophageal cancer. Therefore patients need to be monitored closely and followed up with periodic endoscopic biopsies for the development of dsyplasia (precancerous change) and early adenocarcinomas (cancers). The choice of therapy for Barrett's esophagus mainly depends on the existence and grade of dysplasia (precancerous change).