A man known to have familial dysautonomia presented with a cardiac arrhythmia due to development of hiatal hernia and gastroesophageal reflux. Preoperative symptoms and assessment are described including use of power spectrum analysis of heart rate fluctuations which was consistent with enhanced parasympathetic stimulation. After surgical repair of hiatal hernia and fundoplication, bradycardia resolved, gastroesophageal reflux symptoms subsided, and the power spectrum analysis of heart rate confirmed decreased parasympathetic influence. Power spectrum analysis proved to be a useful adjunct in confirming preoperative autonomic imbalance and assessing the postoperative result. It is concluded that in individuals with disorders such as familial dysautonomia that are associated with autonomic dysfunction, cardiac arrhythmias may be a sign of esophageal pathology. Thus, cardiac evaluations should be accompanied by investigation of gastroesophageal structure and function and appropriate treatment may prevent a catastrophic arrhythmia.