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1 Achalasia. 2  Achalasia is a condition that affects the smooth muscle portion of the esophagus, that is, the lower esophagus and the lower esophageal sphincter. 3  Specifically, the peristaltic wave disappears, and the lower sphincter does not relax.
Disorders of the nervous system can also cause muscles to twitch. These include nerve damage, fibromyalgia, muscular dystrophy and Lou Gehrig's disease. Along with muscle twitching, weakness in the muscles accompanies these disorders.