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The stomach has six different sets of glands, and the most important substances they secrete are hydrochloric acid (HCl) and a number of enzymes, including pepsin, which digest protein. These enzymes need an acid environment in order to break the amino acid bonds. The stomach actually begins secreting HCl and other enzymes while protein food is still being chewed, as the body reacts to the sight and taste of the food. The first stages in the digestion of protein can take several hours after which the partially digested food passes into the small intestine where further breakdown of the amino acids takes place as the pancreas secretes the enzyme protease.

Experiments with animals have shown that the stomach has a built-in timetable for gastric secretion. When bread, which contains both carbohydrate and protein, is swallowed, little HCl is released at first while a large amount of pepsin keeps the climate in an alkaline condition and allows ptyalin to continue digesting the starch. Meanwhile, the pepsin begins working on the protein. Once the carbohydrate process is near completion, more gastric juice is released that rapidly accelerates the digestion of the protein. It was also discovered that foods arranged in the stomach remain in the order they are eaten even while the contents are being churned; and liquids consumed while food is in the stomach pass around the food mass and enter the small intestine.

Liquid alone leaves the stomach rather quickly unless it is a thick mixture or puree. Fruits are next, then vegetables, unless eaten with fat or sauces, followed by starches, and then starches mixed with legumes or meats because of the added protein content. Fats take the longest and slow emptying of the stomach if combined with any other food. Stimulants such as coffee, tea, and strong spices can hasten emptying time of the stomach and may also affect digestion by irritating the stomach walls. Certain food additives and excess salt may have the same effect.

Cells in the stomach also secrete mucus. Mucus inhibits the gastric acids from digesting the stomach itself. The mucus constantly flows across the surface of the stomach to maintain the acid and enzyme balance. Too much acid can result in an irritated or ulcerated stomach. Overabundance of mucus, however, can encourage bacterial growth because gastric acid is necessary to keep the intestinal tract free of bacteria. It is estimated that nearly half of the population may be deficient in HCl, especially among the elderly.

After one to four hours, depending on the combination of foods ingested, peristalsis pushes the food, now in the liquid form of chyme, out of the stomach and into the first part of the small intestine through a valve called the duodenum. The pancreas secretes proteolytic enzymes in varying proportions depending on what kind of food is present. If there is any fat, bile, which is produced by the liver from cholesterol, is released from the gallbladder where it has been stored. Bile disperses the fat globules into small droplets so that the pancreatic enzyme lipase can break them down into fatty acids.

If bile contains large amounts of cholesterol, crystals or stones can form in the gallbladder. The crystals obstruct the flow of bile into the small intestine and inhibit fat digestion. Cholesterol levels rise, and if the stones become so large they completely block the bile ducts, pain results. After the bile salts are finished they are transported out of the body through the elimination tract. Quick exit time through bowel action decreases the amount of cholesterol that remains in the body as bile salts. If contents of the bowel move more slowly, the cholesterol can be reabsorbed and recirculated in the system.

Food molecules continue to be broken down as they move along the remaining 20 ft or so of the small intestine, which is lined with millions of fingerlike projections called villi that give a furlike appearance. These villi contain microvilli which greatly increase the surface area available for absorption. Nutrients are absorbed by the villi and carried through their tiny blood vessels into the bloodstream. Normally, the villi act as a filter and barrier for undesirable and harmful elements by preventing their absorption. However, this defense mechanism can be compromised and weakened by a number of conditions including chronic irritation from harsh stimulants, undesirable microbes, pharmaceutical and recreational drugs, pesticides used on foods, and other environmental pollutants.

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