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When the food leaves the stomach it goes into the small intestine, which is the part of the digestive tract where most of digestion and absorption takes place. The small intestine of an adult male averages about 7m in length and 2-3cm in diameter. Structurally, it is a tubular organ, which consists of a complex system of loops and coils, and fills a large part of the abdominal cavity. The function of the small intestine is to receive secretions from the liver and the pancreas, finalize the digestion of the nutrients in chyme, absorb the different products of digestion, and move the remaining residues to the large intestine.

It is made up of three major parts: duodenum, ileum, and jejunum. A double-layered fold called mesentery connects all of the three.

The small intestine has a very large surface area, because this is where the products of digestion are absorbed. The inner lining of the small intestine has a lot of folds and ridges, and small finger-like growths called villi. The villi have cells that produce intestinal enzymes, which complete the digestion. The base of the villi secretes large amounts of a watery fluid. The fluid acts as a vehicle for moving the digestive products into the villi. Once it is released it serves as a medium in which the digestive products can move, and as soon as they enter the fluid, it is being moved back into the villi.

The upper part of the small intestine, the duodenum, is the most active during digestion. Secretions like bile from the liver, and digestive enzymes and acid-neutralizing bicarbonate from the pancreas, are used for digestion in the duodenum.

Carbohydrates, proteins, and fats are still digested in the small intestine. The carbohydrates starch and glycogen are being broken down into maltose. The proteins are being broken down into small peptide fragments and some amino acids by proteases (enzymes secreted from the pancreas). Bile liquidates fats, facilitating their breakdown until they can be acted upon by lipases. Unlike carbohydrates and proteins, fats are completely digested in the small intestine.