The stomach contains strong acid necessary for digestion. The stomach connects to the esophagus which allows food to pass from the mouth. At the level of your Adam's apple the windpipe(trachea) departs along side of the esophagus and allows air to ventilate the lung. When everything works well the acid is kept in the stomach at all times. Sometimes however at night and while lying down stomach acid and vomit can wash back to the Adam's apple spilling into your voice box and windpipe, causing hoarseness and coughing. This condition can go on for months with only occasional reflux. Please see "Neck Cough: General Therapy" and "Neck Cough: Stomach Reflux and Heartburn".