Lipid digestion begins to occur in the mouth because of the enzyme lipase. Saliva in the mouth incorporates both lipase, to begin lipid digestion, and amylase, to being carbohydrate digestion. Lipids are also broken down later in the digestive pathway by lipase in the small intestine. Protein digestion does not begin until food enters the stomach.

Vitamins A, D, E, and K (ADEK) are fat soluble vitamins, and require the ingestion and absorption of fat in order to maintain adequate stores of the vitamins in the body. Any problems with bile salt function or absorption of bile salt and fat miscelles in the small intestine can lead to a deficiency in vitamins A, D, E, and K. All other vitamins can be absorbed without the help of fat.

The gastrointestinal, or digestive, system is primarily designed to break down (catabolize) nutrients and absorb them into the blood for use by the body. Digestion of nutrients by stomach and pancreatic enzymes allows for their absorption in the small intestine. The large intestine is responsible for water absorption.

Filtration occurs in three primary areas in the body: the kidney, the liver, and the spleen/lymph nodes. The kidney is part of the excretory system, in which fluids are filtered from the blood to remove solute waste from the body. The liver filters the blood in circulation, and is responsible for removing toxins that may have been absorbed during digestion. It is not, however, part of the gastrointestinal tract. The spleen and lymph nodes filter the interstitial fluid to screen for antigens and pathogens.

The hormone aldosterone is most frequently associated with the kidney and nephron function, but has effects on water balance in other regions of the body as well. In the mouth, aldosterone acts on salivary glands to promote sodium and water absorption. The sodium is pumped across the epithelial cells of the mouth, and is able to directly enter the blood via sodium-potassium ATPase function. Potassium is secreted as a result.

The esophagus contains both striated (skeletal) muscle and smooth muscle. The two types of muscle, therefore, allow two distinct functions. Skeletal muscle, in the upper part of the esophagus, allows for voluntary control of swallowing; thus, when a bolus of food has been broken down by chewing, a person can consciously make a decision to begin the swallowing process. Once in the esophagus and past the striated muscle of the upper esophagus, the muscular control is smooth muscle. Smooth muscle is autonomically regulated, meaning that no voluntary control is needed to continue swallowing. Once the food enters the esophagus, the smooth muscle will propel it downwards towards the stomach. The mix of striated and smooth muscle allows for voluntary control of beginning to swallow, but automatic control for swallow completion.

The parasympathetic nervous system, controlled in the gastrointestinal system by the vagus and pubic nerves, serves to decrease the rate of digestion. Rhythmic contractions of the small intestine and large intestine are slowed under parasympathetic control, leading to decreased digestion and absorption of food contents. This represents the "rest and digest" portion of the parasympathetic nervous system, in contrast to the "fight or flight" portion of the sympathetic nervous system.

The parasympathetic nervous system slows digestion, allowing for more absorption of nutrients. The sympathetic response increases the rate of flow through the digestive tract, limiting the amount of absorption that can occur.

The interstitial cells of Cajal link the parasympathetic nervous system with the smooth muscle of the gastrointestinal system. They are responsible for the rhythmic contractions of the gastrointestinal system that propel digested food, and are found in the stomach, small intestine, and large intestine. Interference with their "pacemaker-like" function can lead to constipation and gastroparesis (failure of the gastrointestinal system to contract).

Absorption of fats, iron, and proteins occurs in the small intestine with the aid of microvilli.

Afferent fibers carry information from the periphery to the central nervous system. In contrast, efferent fibers carry information from the central nervous system to the periphery. Generally, afferent fibers will carry sensory information and efferent fibers will carry motor and stimulatory information.

Afferent fibers in the digestive tract will detect changes in content and volume contained in the lumen of digestive organs. These signals are integrated in the central nervous system, and efferent signals are used to promote hormone or enzyme secretions and smooth muscle contraction.

Auerbach's plexus, also known as the myenteric plexus, is located between the gastrointestinal circular and longitudinal muscles, and controls motility throughout the system.

Secretion and blood flow in the gastrointestinal tract are both functions of the submucosal (Meissner's) plexus of the gastrointestinal system. Neither plexus is involved in hormonal balance. 

The vagus nerve is an essential part of the parasympathetic nervous system originating from the brain (cranial nerve X). The vagus nerve innervates the esophagus, stomach, pancreas, and upper portion of the large intestine. It is involved in parasympathetic stimulation of digestive function during periods of "rest and digest."

The rectum is innervated by the pelvic splanchnic nerves, which are also part of the parasympathetic nervous system.