A faulty valve. The main cause of acid reflux disease is a problem with the lower esophageal sphincter (LES) muscle. This muscle, which is the âvalveâ between the stomach and the esophagus, normally closes tightly after food has passed through to the stomach. The LES does not stay closed in people with acid reflux disease. When this happens, acid and stomach contents may back up (reflux) into the esophagus.