This important body system digests food by breaking it down into nutrient molecules small enough to pass into the bloodstream. Nutrient molecules are absorbed in the small intestine and sent into the blood circulatory system. The digestive system also eliminates solid waste, recycles water, and absorbs vitamins from nutrients in the large intestines. Even though some starch breakdown takes place in the mouth and some breakdown of protein is done in the stomach, most of the digestion occurs in the duodenum.

The small intestine is a coiled, tube-like organ held in place by two membrane sheets attached to the walls of the abdominal cavity and referred to as the mesentery. Nerves, blood and lymph vessels to and from the small intestine lie between the two sheets of the mesentery. In the adult, the small intestine measures on average about 22 ft (6.7 m) with a diameter of 1–2 in (2.5–5 cm). It consists of three segments: the short duodenum, the jejunum, which represents 40% of the small intestine, and the terminal ileum, which accounts for the remaining 60% and which empties into the large intestine. The small intestine thus forms a passage going from the pylorus (opening from the stomach) to the large intestine.

The inner mucous membrane of the small intestine is not flat and uniform but folded to such a great extent that its inner lining is referred to as the mucosal folds. The mucosal folds are covered with approximately 20,000 tiny hair-like projections called villi that are lined with epithelial cells studded with microvilli. One villus contains about 500 microvilli and in one square inch of small intestine, there are some ten billion microvilli.

Together, the intestines process 2–3 gal (7.6–11.4 l) of food, liquids, and bodily waste every day. The small intestine is the major site of absorption of almost all nutrients into the blood.

The stomach delivers foodstuffs to the duodenum that it has reduced to a liquid pulp with gastric juices, called the chyme, for further breakdown. The duodenum also receives pancreatic enzymes from the pancreas and bile from the liver via the pancreatic and common bile ducts. The pancreatic enzymes are required for the chemical breakdown of fats, sugars, and proteins, and the bile plays an important role in the absorption of fats. To assist the process, the villi sway constantly so as to stir up the chyme for nutrient removal and transport across their membranes into the blood and lymph vessels. The fatty molecules are transferred to the lymph, while sugar (glucose) and amino acids go into the blood and are carried to the liver. The muscles that encircle the small intestine constrict about seven to twelve times a minute to shake, knead, and mix the chyme with its secretions and the gastric juices of the stomach. The small intestine also absorbs enormous quantities of water. Normal water intake for an adult is about 0.5 gal (2 l) of dietary fluid per day. An additional 1.6–1.8 gal (6–7 l) of fluid is delivered to the small intestine by secretions from salivary glands, stomach, pancreas, liver, and its own secretions. Of these 2.1–2.3 gal (8–9 l), the small intestine absorbs 80% on a daily basis.

The absorption of nutrients across the epithelial cell boundary of the small intestine is made possible by maintaining a "sodium electrochemical gradient." The interior of all cells maintains a low concentration of sodium. The epithelial cells lining the small intestine (enterocytes) achieve this using a large number of enzymes (Na+/K+ ATPases), called sodium pumps. These pumps export sodium ions from the cell in exchange for potassium ions, thus establishing a gradient of both charge and sodium concentration across the cell membrane that facilitates transport. This constant flow of sodium is ultimately responsible for the absorption of water, amino acids, and carbohydrates by the small intestine. It is known that each intestinal enterocyte has some 150,000 such sodium pumps, which allow each cell to transport about 5 billion sodium ions out of each cell per minute.

The passage of foodstuffs through the small intestine results in the absorption of most of the water and electrolytes (sodium, chloride, potassium) as well as almost all nutrient molecules, such as glucose, amino acids, and fatty acids. The small intestine not only provides the nutrients required for the functioning of the body, but also plays a critical role in water and acid-base equilibrium. Acid-base equilibrium refers to a condition by which the net rate of acid or base production by the body is balanced by the net rate of acid or base elimination from the body, resulting in stable amounts of hydrogen ions in body fluids.

The common diseases and disorders of the small intestine include:

* Adenocarcinoma. Adenocarcinomas are cancers of the gland cells that line the small intestine. They tend to occur in the duodenum.
* Adenomas. Adenomas are non-cancerous gland cell tumors often found in the intestinal villi.
* Atresia of small intestine. Atresia of the small intestine is characterized by the absence or closure of parts of the small intestine. Duodenal atresia is diagnosed in 1:5,000 live births and is frequently associated with Down syndrome. Jejuno-ileal atresia occurs less frequently (1:1,500 to 1:20,000 live births).
* Carcinoid tumors. Carcinoid tumors develop from the neuroendocrine cells that are found in the numerous secretions entering the intestine. About 2,500 carcinoid tumors are diagnosed each year in the United States and they account for about one-third of all tumors that develop in the small intestine and appendix.
* Crohn's disease. Crohn's disease causes inflammation in the small intestine. It usually occurs in the ileum.
* Cytomegalovirus (CMV). CMV is a herpes-type virus that can infect the epithelial cells of the small intestine.
* Duodenal ulcer. Gastric and duodenal ulcers afflict approximately 4 million people in the United States. They are associated with alcoholism, chronic lung and kidney disease, and thyroid disorders.
* Dysentery. Dysentery is a general term for various disorders characterized by severe diarrhoea, inflamed intestines, and intestinal bleeding. Some forms of dysentery may clear up by themselves while other forms may continue for years without treatment.
* Protein-losing enteropathy. Disease of the small intestine characterized by excessive loss of plasma proteins.
* Gastrointestinal stromal tumor (GIST). GIST is most commonly diagnosed in the muscular wall of the jejeunum and ileum.
* Gluten sensitive enteropathy. Disease of the small intestine characterized by impaired absorption of nutrients due to loss of villi because of an adverse immune reaction to gluten, a protein found in wheat and other related foods.
* Small intestinal hemorrhages. The major causes of small intestinal hemorrhage are infections, vascular anomalies, and bleeding disorders.
* Small intestinal infarction. Small intestinal infarction is caused by the partial or complete obstruction to blood flow. It usually occurs in people over age 50–55.

Inestigating the small bowel can involve any of the following tests :-

1) Upper endoscopy and duodenal biospy
2) Small bowel follow-through (or Small bowel enema)
3) CT enteroclysis
4) Capsule endoscopy
5) Glucose Hydrogen Breath test
6) Laparoscopy