It usually takes about one to three days (though a week or longerToxinsInTheBody resized 600 wouldn’t be abnormal) for food to pass completely through your body. Inside your gastrointestinal tract are lots and lots of bacteria that help break down the food, retrieve nutrients and destroy toxins. A milliliter of fluid from your small intestine contains about 10,000 microorganisms. Bacteria are most abundant in your colon, which has about 1 billion bacteria per milliliter [source: Dennis Lee, MD]. Not only do the colon and small intestine contain vastly different quantities of bacteria, they also contain different types. These bacteria are good for you, and your immune system leaves them alone.

Your intestinal muscles usually move bacteria along, but if they don’t (due to a medical condition such as diabetes), bacteria multiply and grow. If too much bacteria grows in the small intestine, or if the type of bacteria that grows in the colon is found in the small intestine, problems such as bloating, discomfort, diarrhea and constipation can arise.

Your body’s own bacteria aren’t the only things that can get your digestive system out of whack. Toxins and even parasites can enter your body through diet, respiration and environmental factors. Most toxins break down in the digestive process, and parasitic infections usually resolve themselves in time, but that isn’t always the case.

Leftover toxins can be absorbed through your intestines, giving them the freedom to cause physical and neurological distress. Proponents of colon cleansing believe you can lessen or prevent the chance of absorption through colon cleansing.

Source: http://health.howstuffworks.com/medicine/surgeries-procedures/colon-cleansing-good1.htm