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Diagnostics > Colonoscopy

Colon cleansing and intestinal rehabilitation: What’s the difference?

Dr. med. André Sommer

Dr. med. André Sommer

The concept of intestinal rehabilitation comes from alternative medicine. In natural medicine, the gut is the most important organ in the immune system. That's why it is thought to be responsible for the development of many diseases. In alternative medicine, intestinal rehabilitation is used not only to treat gastrointestinal diseases but also in the treatment of allergies, infections, and rheumatic diseases. Colon cleansing is more of a term in conventional medicine and is used, for example, when preparing the colon for a colonoscopy. Intestinal rehabilitation has not found its way into evidence-based conventional medicine.

What is intestinal rehabilitation?

Up 100 trillion bacteria live in a person's gut. Much more than there are cells in the human body. Most of these bacteria belong to the natural intestinal flora and live in symbiosis with the human body (host): the bacteria and the human body benefit from living together.

The bacteria are supplied by the food in the intestine, and in return they produce useful nutrients (such as short-chain fatty acids and vitamin K) which are used by the body. The natural intestinal flora also helps to develop our immune system. Through constant contact with bacteria, it learns to differentiate between harmful and non-harmful organisms and thus to fight them better and faster.

In naturopathy it is assumed that an imbalance is the cause of many diseases in the normal intestinal flora. If there are more harmful bacteria or harmful fungi in the intestine, the natural balance is disturbed and the interaction between intestine and intestinal bacteria no longer works.

Intestinal rehabilitation should help to restore the balance through various measures and thus eliminate the shift in the intestinal flora as the cause of many diseases.

What is the difference between intestinal rehabilitation and colon cleansing?

The term “intestinal rehabilitation” describes a naturopathic concept to normalize a disturbed intestinal flora through therapeutic measures and thus alleviate diseases.

The term colon cleansing in conventional medicine only describes the process of cleaning the colon, for example by enemas and laxatives. Colon cleansing may be necessary before medical procedures. For example, patients who have a colonoscopy, drink laxative liquids before the examination to cleanse the intestine. Colon cleansing can also be part of intestinal rehabilitation therapy. Intestinal rehabilitation in alternative medicine means the cleansing of the intestines from harmful substances.

What causes an imbalance in the intestinal flora?

The intestinal flora of every person is different. It develops over the course of life and is influenced by our lifestyle, diet, and environment. The exact composition of the intestinal flora is subject to constant change.

Intestinal rehabilitation due to improper nutrition

A change in eating habits may cause the composition of the intestinal flora to change. This has been demonstrated, for example, in the low-FODMAP diet.

Intestinal rehabilitation due to gastrointestinal infections and antibiotics

Infectious diseases can also cause certain bacteria to spread and displace others. A well-studied example of a drastic change in the intestinal flora is antibiotic therapy. In rare cases it can happen that the antibiotics, which kill bacteria, destroy a large part of the intestinal flora. However, the bacterium named Clostridium difficile often survives antibiotic therapy and then multiplies unchecked. This causes inflammation of the intestine (enteritis), which can only be remedied by deliberately destroying C. difficile.

Intestinal rehabilitation due to improper colonization

The small intestine, which actually has far fewer bacteria than the large intestine, can be colonized by too many and the wrong bacteria due to certain influences. This is referred to as improper colonization.

In alternative medicine, fungi are often considered the reason for intestinal rehabilitation. According to this theory, an overgrowth of the intestine with fungi leads to a shift in balance. The modern, sugar-rich diet is primarily responsible for this. It provides fungi such as the yeast candida albicans optimal propagation conditions. In conventional medicine, candida albicans does not play a role in the development of the disease in the intestine.

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How is intestinal rehabilitation carried out?

A classic intestinal rehabilitation in the naturopathic sense usually consists of three steps:

  • Introductory intestinal rehabilitation with laxatives
  • Eliminating harmful germs (especially fungi)
  • Probiotic therapy, which promotes the growth of the natural intestinal flora

1. Introductory intestinal rehabilitation

Intestinal rehabilitation often starts with cleansing the intestine. Either natural laxatives such as Epsom salts and Glauber salts are used for this, or the intestine is cleansed directly with the help of enemas (colon hydrotherapy).

2. Eliminating harmful germs

The elimination of harmful germs is primarily directed against fungi that affect the intestine. Usually the drug nystatin is administered as a tablet or drinking solution. It kills fungi by damaging their cell membranes. Since nystatin cannot be absorbed by the body, it only works in the gastrointestinal tract. Treatment with nystatin usually takes place over two weeks.

In addition, an antifungal diet is recommended. Since intestinal fungi mainly feed on sugar, care should be taken during this phase to eat a low-sugar and low-carbohydrate diet—similar to the low-carb diet. The most important foods to avoid are table sugar, fructose, honey, and other sugars like sorbitol, mannitol, and dextrose.

3. Probiotic therapy

Probiotic therapy should help to build a healthy intestinal flora. To do this, various benign strains of bacteria are administered as tablets (probiotics). The most common bacterium used is escherichia coli (E. coli).

Is intestinal rehabilitation recommended by doctors?

There is a great deal of disagreement among naturopaths and conventional doctors about whether intestinal rehabilitation is really helpful or not. Naturopathy has long sworn by the healing power of intestinal rehabilitation. They often refer to patient reports and the fact that intestinal rehabilitation was successfully used in the Middle Ages and in traditional medicine.

Trained Western doctors often regard intestinal rehabilitation as treatment for diseases with a critical eye. There are no good studies that prove the positive effect of intestinal rehabilitation. In addition, many cases are described in which the intestinal rehabilitation measures, especially colon hydrotherapy, lead to damage to the intestine.

Since there is no evidence of the effectiveness of intestinal rehabilitation, the cost of such therapy is not covered by insurance. However, it is agreed that the intestinal flora (microbiome) has a greater impact on the body than previously thought. There is currently a lot of conventional medical research on how to specifically influence the intestinal flora without harming people.

Does intestinal rehabilitation help with IBS?

There is also disagreement as to whether intestinal rehabilitation helps against the symptoms of IBS. Naturopaths report about patients in whom such remedial treatment has led to the improvement of symptoms. Trained western doctors are rather skeptical about this claim and do not recommend intestinal rehabilitation for IBS.

However, the fact that a change in diet, probiotics, psychotherapy and exercise can have positive effects on IBS symptoms is also accepted by conventional doctors. Therapy for IBS should be done in consultation with a doctor.


Intestinal rehabilitation is a controversial treatment in medicine. Many patients report success, but the risks of such therapy are also known. It is advisable to carry out intestinal rehabilitation only in consultation with the doctor treating you, in order to be able to react quickly to possible complications. In the end, intestinal rehabilitation can help to alleviate symptoms caused by gastrointestinal diseases.

Ernst, E. (2010). Colonic irrigation: therapeutic claims by professional organisations, a review. International journal of clinical practice, 64(4), 429-431. Link:, downloaded on 19.06.16

Mishori, R., Otubu, A., & Alleyne Jones, A. (2011). The dangers of colon cleansing. Journal of Family Practice, 60(8), 454. Link:, downloaded on 22.06.16

Ernst, E. (1997). Colonic irrigation and the theory of autointoxication: a triumph of ignorance over science. Journal of clinical gastroenterology, 24(4), 196-198. Link:, downloaded on 23.06.16

Gardiner, A., Marshall, J., & Duthie, G. (2004). Rectal irrigation for relief of functional bowel disorders. Nursing Standard, 19(9), 39-42. Link:, downloaded on 19.06.16

Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207-214. Link:, downloaded on 19.06.16

Dr. med. André Sommer

Dr. med. André Sommer

I’m André, a medical doctor from Berlin. Together with a team of medical doctors, nutritionists and data scientists we empower people to understand digestive issues with our app Cara Care.

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