Gut basics
The small intestine: digestion and nutrient absorption explained
The small intestine is where digestion is completed and where almost all nutrients are absorbed. It is a coiled tube several metres long, with three parts: the duodenum, the jejunum and the ileum. When it is damaged or overgrown with bacteria, the results are bloating, loose stools, weight loss and nutrient deficiencies.
In short
- The small intestine absorbs nearly all the carbohydrate, protein, fat, vitamins and minerals you eat.
- Its inner surface is folded into millions of finger-like projections, which give it a very large area for absorption.
- Different nutrients are absorbed in different sections.
- Coeliac disease, infections, bacterial overgrowth and Crohn’s disease are the main conditions that affect it.
What are the three parts, and what does each do?
| Part | Main jobs |
|---|---|
| Duodenum (first 25 cm) | Receives food from the stomach, bile from the liver and enzymes from the pancreas. Absorbs iron and calcium. |
| Jejunum (middle) | Absorbs most sugars, amino acids, fats and vitamins. |
| Ileum (last part) | Absorbs vitamin B12 and bile salts, and whatever the jejunum has left. |
This is why disease or surgery affecting the ileum leads to vitamin B12 deficiency, and why iron deficiency is a common sign of coeliac disease, which damages the upper intestine.
How does absorption work?
The lining is covered with tiny projections called villi, and each cell on them carries even smaller projections. Enzymes on this surface complete the last step of digestion, and the cells then pass nutrients into the blood. The blood flows first to the liver.
The small intestine normally contains few bacteria compared with the colon. Stomach acid, bile, steady forward movement and a valve at its lower end keep it that way.
What can go wrong?
Coeliac disease
A reaction to gluten flattens the villi and reduces the absorbing surface. See gluten sensitivity.
Bacterial overgrowth (SIBO)
Bacteria multiply in the small intestine and ferment food before it is absorbed. See SIBO.
Infections
Giardia and other infections damage the lining. A long-lasting form after tropical infections is called tropical sprue.
Lactose intolerance
The enzyme that digests milk sugar is low or absent. See lactose intolerance.
Crohn’s disease
Inflammation, most often of the ileum. See inflammatory bowel disease.
Disease of the pancreas or bile flow
Without enzymes or bile, fat is not digested and passes into the stool.
What are the signs of poor absorption?
- Loose, bulky, pale or oily stools that are difficult to flush
- Bloating and excess gas
- Weight loss despite eating normally
- Tiredness, with anaemia from low iron, vitamin B12 or folate
- Mouth ulcers, a sore tongue, tingling in the hands and feet
- Bone pain or fractures from low vitamin D and calcium
- In children, poor growth
Which tests are used?
Blood tests show anaemia and vitamin levels and screen for coeliac disease. Stool tests look for infection and fat. A breath test detects bacterial overgrowth and lactose malabsorption. An endoscopy with tissue samples from the duodenum confirms coeliac disease and other causes. Scans examine the rest of the small intestine.
How do I look after my small intestine?
Treatment of a specific condition comes first. Beyond that, the functional medicine sequence applies: remove what is injuring the lining, such as an infection or an offending food; replace what digestion lacks; restore a healthy balance of bacteria; and give the lining the protein and nutrients it needs to repair. The lining renews itself every few days, so it recovers well once the cause is removed.
Questions patients ask me
Can I be deficient in vitamins even though I eat well?
Yes. If the lining is damaged or bacteria are consuming nutrients first, a good diet may not be enough. Unexplained deficiencies are a reason to look at the small intestine.
How long does the lining take to heal?
The surface cells are replaced every three to five days. After an infection it recovers within weeks. In coeliac disease, healing on a gluten-free diet takes months to a couple of years.
Is bloating a sign of a small intestine problem?
It can be, particularly when it comes with loose stools or follows meals rich in fermentable carbohydrate. Bloating has other causes too. See bloating.
Sources
This page is written for patients and is based on the guidelines and studies below. It is for education and does not replace a consultation.
- American College of Gastroenterology guideline on coeliac disease. Rubio-Tapia A et al. Am J Gastroenterol. 2023. PubMed 36602836
- American College of Gastroenterology guideline on small intestinal bacterial overgrowth. Pimentel M et al. Am J Gastroenterol. 2020. PubMed 32023228
- Review of lactose malabsorption and intolerance. Misselwitz B et al. Gut. 2019. PubMed 31427404
- European Crohn’s and Colitis Organisation guideline on medical treatment in Crohn’s disease. Torres J et al. J Crohns Colitis. 2020. PubMed 31711158