1 Many medications can cause diarrhea. 2  The most common are antibiotics. 3  Antibiotics destroy both good and bad bacteria, which can disturb the natural balance of bacteria in your intestines. 4  This disturbance sometimes leads to an infection with bacteria called Clostridium difficile, which also can cause diarrhea. Many medications can cause diarrhea. 2  The most common are antibiotics. 3  Antibiotics destroy both good and bad bacteria, which can disturb the natural balance of bacteria in your intestines. 4  This disturbance sometimes leads to an infection with bacteria called Clostridium difficile, which also can cause diarrhea.
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