When you swallow a pill, what happens to it? After being swallowed, a pill travels down the esophagus, which connects the mouth to the stomach. Once the pill reaches the stomach, stomach acid dissolves it. The dissolved medication passes from the stomach into the small intestine. It is then absorbed into the blood vessels surrounding the small intestine. Once the medication enters the blood stream, it circulates and is carried to all the organs of the body to help the healing process.