Many medications cause diarrheal side effects. Antibiotics are one of the most common causes of diarrhea. They affect the flora and the bacteria in the GI tract, and that can subsequently allow patients to have diarrhea. The good thing about many medications that have that diarrheal side effect is that once you stop the medication, those symptoms usually go away. Some antibiotics cause a disorder called C diff infection, which is when your bacteria in your GI tract, the flora gets altered and a specific bacteria called C diff starts growing more than the surrounding bacteria, and that can end up having a diarrhea that requires subsequent antibiotic therapy.