There are many possible reasons. Sometimes you need the drug to be absorbed through the stomach or intestines relatively quickly, without any food competing for passage and slowing absorption of the drug. Sometimes you actually want the opposite, where the drug breaks down and gets absorbed slowly as you digest the food around it. Sometimes the drug actually interacts with some foods that you might eat, reducing its effectiveness. Sometimes the drug irritates your stomach, and having food there can reduce the irritation. It depends a lot on how the drug works and how much your body tolerates it.
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