Some forms of colon hydrotherapy use tubes to inject water, sometimes mixed with herbs or with other liquids, into the colon via the rectum using special equipment. Oral cleaning regimes use dietary fiber, herbs, dietary supplements, or laxatives. People who practice colon cleansing believe that accumulations of putrefied feces line the walls of the large intestine and that these accumulations harbor parasites or pathogenic gut flora, causing nonspecific symptoms and general ill-health. This "auto-intoxication" hypothesis is based on medical beliefs of the Ancient Egyptians and Greeks and was discredited in the early 20th century.

No scientific evidence supports the alleged benefits of colon cleansing. The bowel itself is not dirty and barring drugs, disease or mechanical blockage, cleans itself naturally without assistance. Certain enema preparations have been associated with heart attacks and electrolyte imbalances, and improperly prepared or used equipment can cause infection or damage to the bowel. Frequent colon cleansing can lead to dependence on enemas to defecate and some herbs may reduce the effectiveness of prescription drugs.