What Causes Diarrhea in Dogs? "There are many causes of diarrhea in dogs," says Dr. Jennifer Coates. "The most common are intestinal parasites (e.g., roundworms, hookworms, Giardia), bacterial infections or overgrowth, dietary indiscretion (e.g., garbage ingestion or an abrupt diet change), and inflammatory diseases (e.g., diet intolerances or allergies)."