The cause of achalasia is unknown. Theories on causation invoke infection, heredity or an abnormality of the immune system that causes the body itself to damage the esophagus (autoimmune disease).

The esophagus contains both muscles and nerves. The nerves coordinate the relaxation and opening of the sphincters as well as the peristaltic waves in the body of the esophagus. Achalasia has effects on both the muscles and nerves of the esophagus; however, the effects on the nerves are believed to be the most important. Early in achalasia, inflammation can be seen (when examined under the microscope) in the muscle of the lower esophagus, especially around the nerves. As the disease progresses, the nerves begin to degenerate and ultimately disappear, particularly the nerves that cause the lower esophageal sphincter to relax. Still later in the progression of the disease, muscle cells begin to degenerate, possibly because of the damage to the nerves. The result of these changes is a lower sphincter that cannot relax and muscle in the lower esophageal body that cannot support peristaltic waves. With time, the body of the esophagus stretches and becomes enlarged (dilated).