The Science Behind Infant Digestion

Moms who are breasfeeding need more water.
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Digestion is defined as the body's process of breaking foods down into components that can be absorbed and used wherever they are needed. Each step takes place in the gastrointestinal (GI) tract, which includes the mouth, esophagus, stomach, small intestine, and large intestine (colon). Several accessory organs—the pancreas, gall bladder, and liver—also play important roles.

Although it may go unnoticed, the first time a newborn digests breast milk or formula is truly a landmark moment. In the womb, digestion is unnecessary. Nutrients from the mother's blood are absorbed via the placenta and umbilical cord into the baby's bloodstream, and waste products are transferred back to the mother's blood by the same route.

Until birth, the GI tract is simply waiting for the right moment to begin doing its job. The first feeding gives an infant's digestive system a jump start, stimulating both intestinal movement and maturation of the entire GI tract. Your baby's diet has an enormous impact on their current growth and development as well as their future health.

The digestion of breast milk or formula not only provides energy for the body, it also allows for the establishment of a healthy gut microbiome. A diverse, thriving microbiome is critical for the immune system and lifelong health.

What is the Gut Microbiome?

The collection of bacteria, viruses, fungi, protozoa, and other microorganisms in the intestinal tract is known as the gut microbiome. It is mostly located in the large intestine.

Your baby's diet has an enormous impact on their current growth and development as well as their future health. Research has found that the composition of gut microflora in infancy has an influence on the future development of a host of autoimmune conditions, including Type 1 diabetes and inflammatory bowel disease.

Proper digestion is also critical for the efficient absorption of nutrients, which has an impact on virtually every aspect of your baby's health. For example, if dietary fats are not fully digested in the GI tract, the omega-3 fatty acids vital for eye and brain development may not be absorbed into the blood and available to serve their functions.

Anatomy of the Digestive Tract

Like many other parts of the human body, the GI tract is not fully mature at birth. Certain enzymes and differences in anatomy mean that digestion is achieved in a slightly different way in newborns, but their bodies are nonetheless well-equipped to break food down into components ready for absorption.

Let's begin by looking at the anatomy of the digestive tract and see what happens from the moment food enters your baby's mouth until it ends up in their diaper. Each section of the GI tract has a specialized structure that allows it to perform distinct roles in the transport and digestion of nutrients.

The GI tract is essentially a long, folded tube that stretches from the mouth to the anus. It has an amazingly large surface area, even larger than that of the skin.

This surface area is due mostly to the villi and microvilli (tiny hair-like structures) that cover the small and large intestine. Once digestion is complete, nutrients are absorbed into the bloodstream, liver, and other destinations through the thousands of square centimeters of tissue provided by the villi and microvilli.


Your baby's mouth plays the role of accepting breast milk or formula. Their jaws and tongue work to draw milk out of the breast or bottle. When they swallow, the tongue pushes fluid to the back of the throat and into the esophagus. A small tissue flap called the epiglottis covers the trachea (or windpipe) during swallowing.

Digestion of carbohydrates (starches and sugars) begins in the mouth once babies reach 3 months of age, thanks to an enzyme called salivary amylase. Because the salivary glands begin secreting amylase as soon as a person anticipates eating, this is considered the first step in digestion.


The tube that connects the mouth to the stomach is called the esophagus. Its job is two-fold: to push food or fluid from the mouth to the stomach and to prevent backflow, or reflux, of stomach contents.

Like the entire GI tract, the esophagus is made up of a series of muscles that contract in a wave-like sequence (called peristalsis) to keep food moving through the GI tract during digestion.

Reflux is prevented by a ring-shaped muscle called the lower esophageal sphincter. This sphincter sits at the bottom of the esophagus, just above the stomach. It relaxes to allow food into the stomach, and then tightens again to prevent it from flowing back into the esophagus.

The lower esophageal sphincter is often weak until one year of age, which is why many young babies have reflux, known as gastroesophageal reflux disease (GERD) if it causes problematic symptoms. But by their first birthday, only 10% of infants still experience this condition.


The stomach is responsible for storing food while it is combined with enzymes and acids for digestion. Gastric acid is made by the liver, stored in the gall bladder, and released into the stomach in response to food intake.

Gastric acid is made up mostly of hydrochloric acid. It is extremely potent, keeping the pH level of the stomach so low that the stomach lining would be burned if it wasn't protected by a thick layer of mucus.

This acidic environment activates digestive enzymes, allowing them to break down food in the stomach. Once food has been adequately digested, the stomach regulates the release of its contents into the small intestine.

Small Intestine

The small intestine is a tube-like organ separated into three parts: the duodenum, jejunum, and ileum. The duodenum is the workhorse of the digestive process, breaking down carbohydrates, protein, and fats. The absorption of many vitamins and minerals takes place in the jejunum and ileum.

Partially-digested food from the stomach is combined in the small intestine with secretions from the pancreas that are delivered through small ducts. The digestive enzymes from those secretions are in charge of most of the digestive process in the small intestine.

Each enzyme acts only on the macronutrient it is meant to digest.

  • Amylase and other carbohydrate enzymes digest carbs into glucose and other simple sugars
  • Lipase breaks fats down into their building blocks, glycerol and fatty acids
  • Protease digests proteins into amino acids

Most of these enzymes are produced by the pancreas.

Bile salts are a type of detergent that enables dietary fat to mix with water in the small intestine so it can be digested by lipase.

The final products of digestion are absorbed into the bloodstream through the villi and microvilli. Anything left behind after nutrients and fluid have been absorbed moves into the large intestine to be passed out as stool.

Large Intestine (Colon)

The colon curves upward from the end of the small intestine, across the abdomen and down to the rectum. It is mostly in charge of the absorption of water and electrolytes.

As waste (or stool) moves through the colon, water and electrolytes are removed so that the stool becomes more solid. By the time it reaches the last section of the colon (called the sigmoid colon), stool is primarily composed of food waste and bacteria. The body holds stool in the sigmoid colon until enough has accumulated to be passed into the rectum for a bowel movement.


The sphincter of O'Beirne regulates the flow of waste from the sigmoid colon into the rectum, which is a holding area for stool. The internal and external anal sphincters regulate the flow of fecal matter from the rectum.

All parts of the digestive system work together to take in food, transport it through the GI system, mechanically and chemically break it down into its component parts, and then eliminate the excess material as waste.

Accessory Organs of the Digestive Tract

In addition to the digestive tract itself, there are several accessory organs that play crucial roles in the digestion of food. These include:

Gall Bladder

The gall bladder is a tiny sac that sits just below the liver. Bile from the liver is collected here and concentrated before being released into the duodenum.

Both the gall bladder and liver are essential for proper digestion and absorption of fats and fat-soluble vitamins, which include vitamins A, D, E, and K.


The liver is the largest organ in the body. It is in charge of protein and carbohydrate metabolism and the storage of glycogen and vitamins. It also aids in the formation, storage, and elimination of bile and plays a role in fat metabolism.

The liver's main digestive function is to process the nutrients absorbed from the small intestine and transform them into chemicals that can be used by the body. The liver is also where toxins, including some drugs, are captured, processed, and stored or excreted to protect the rest of the body.


The pancreas secretes enzymes into the small intestine for the digestion of fats, proteins, and carbohydrates. While digestive enzymes are made in the exocrine pancreas, many people are more familiar with the hormone insulin, which is made in the endocrine glands of the pancreas.

The Importance of Breast Milk in Digestion

Breast milk also contains enzymes which help in digestion, such as amylase, lipase, and protease. This is one reason breast milk is considered the perfect food for newborns, as most of the digestive enzymes are present at very low levels at birth. They rise steadily to adult levels by weaning.

Digestive Differences Between Infants and Adults

Many aspects of infant digestion—including how the GI tract develops—are still a mystery to medical experts. The reason for this knowledge gap is that gastrointestinal research requires invasive procedures that are usually not done on infants unless medically necessary.

What we do know, however, is that infant digestion differs from that of adults in multiple ways. There are several anatomical as well as functional differences between the digestive tract of infants and adults.


In the infant, the tongue is larger in relation to the oral cavity and extra fat pads on the sides of the tongue help with sucking. As noted above, salivary amylase is not present until 3 months of age.

However, babies (unlike adults) do have lipase in their mouths to initiate fat digestion. This enzyme begins to decline in infancy and is not present by childhood.


In a newborn baby, the esophagus is about 4 1/2 inches long (versus 9 1/2 inches long in adults) and the lower esophageal sphincter is around 1/2 inch in diameter. In the throat, the epiglottis lies over the soft palate to supply extra airway protection during swallowing.


The newborn stomach can only hold about 20 ml (just over 1 tablespoon) of fluid. This explains why babies need to eat every couple of hours.

Immediately after birth, a baby's stomach pH is higher than that of adults, around a neutral level of 7. This is due to fetal intake of amniotic fluid, which also has a pH of 7. In comparison, the pH of an adult stomach is between 1 and 2.

A baby's neutral stomach pH allows macronutrients (carbohydrate, fat, and protein) from breast milk or formula to pass into the small intestine without being fully digested, where they are directly absorbed to a greater extent into the blood.

The high stomach pH only lasts a short time, beginning to drop within 24 hours after birth. Fasting stomach pH is between 3 and 3.5 in babies a few days old.

Another age difference is that lipase plays a much greater role in fat digestion in the infant stomach. In adults, lipase is more active in the small intestine.

Studies have found that infants' stomachs empty about twice as quickly after a meal of breast milk compared to one of formula. This provides an explanation for the idea that formula-fed babies sleep longer and/or better than breast-fed infants. They actually feel full longer, allowing them to go for longer stretches between feedings.

Small Intestine

There are differences between the infant and adult small intestine as well. In the infant, it measures between 100 and 120 inches long (8-10 feet) and in the adult, approximately 264 inches (22 feet).

One key characteristic of the small intestine immediately after birth is its increased permeability. Large molecules (proteins and carbohydrates, for example) can easily pass through the small intestinal wall for a short time after birth, but that quickly changes as gaps in the wall close.

Immunoglobulins are an immune protein that protects infants from illness. Because babies do not have a strong immune system at birth, they rely on immunoglobulins from their parent's breast milk to help get it established. One reason why the small intestinal wall may be more permeable just after birth is to maximize the transfer of immunoglobulins from breast milk to the infant's body.

Research is ongoing to determine how long this window lasts. We do know that once the stomach and pancreas begin making peptidases (a type of protein-digesting enzyme) soon after birth, the amount of proteins that reach the small intestine intact drops sharply.

In infants, bile salts play a prominent role not only in fat digestion, but also in clearing the body of bilirubin (to prevent jaundice), maturation of the GI tract, and the establishment of good bacteria in the gut.

While bile salt production is fairly low in infants, their small intestine can reabsorb bile from the blood. This is essentially the newborn's way of recycling its bile salts for use until the liver is able to make it in adequate amounts. Interestingly, breast milk contains both bile salts and lipase to aid in fat digestion.

Another of the many enzymatic differences is that infants produce more carbohydrate-specific enzymes than adults do. This enables their bodies to digest the high levels of lactose and other sugars found in breast milk and formula.

Once solid foods are started and babies are weaned, their intestinal and pancreatic enzyme profile changes to look much more like that of an adult.

Large Intestine

The colon plays a much greater role in the absorption of nutrients in newborns than it does in adults. Researchers think this may be the body's way of compensating for the limited absorption that takes place in the small intestine in the neonatal period (after the brief window of permeability has closed).


The first stools passed are called meconium. Meconium is thick, sticky and tarlike. It is black or dark green in color and made up of mucus, vernix (the white cheesy substance present on a baby's skin), lanugo (the fine hairs present on a baby's skin, especially in preemies), hormones, and carbohydrates.

It is extremely necessary that a newborn baby passes stool within 24 hours of birth.After meconium has been excreted, parents will notice that their baby's stools are softer than an adult's. This is because babies drink only breast milk or formula for about the first 6 months of life.

Not only is their diet entirely liquid, but it also contains negligible amounts of fiber and no solid proteins (such as those in meat and eggs.) These dietary components are responsible for creating most of the bulk in the stool of an older child or adult.

When babies begin eating solid foods, their stools will become more solid as well.

Healthy Gut Bacteria

In recent years, research has greatly advanced our knowledge about gut bacteria and their importance in everything from physical health to emotional well-being. The health of a baby's gut will influence not only their current growth, but their overall health for years to come.

It was previously thought that the GI tract was sterile at birth. However, studies have now determined that it is colonized with bacteria in the womb as a result of the placenta and the ingestion of amniotic fluid.

Although the gut microbiome of infants is not as diverse as that of adults, it is rapidly colonized soon after birth from sources such as breast milk, probiotics, and other external bacteria and viruses. The establishment of a healthy gut microbiome in the first few years of life is critical for continued health later in life.

In addition to digestive enzymes, healthy gut bacteria are important in the proper digestion and absorption of nutrients. Fats and a special type of carbohydrate called oligosaccharides serve as food for gut bacteria in the infant, allowing the bacteria to reproduce as they take part in the digestive process.

The oligosaccharides found in high levels in breast milk are though to be responsible for colonizing up to 90% of the infant gut microbiome.

Gut bacteria also work to synthesize the B vitamins and vitamin K, which plays a vital role in blood clotting. In addition, they ensure that the immune system works properly. Breastfed infants receive natural probiotics and oligosaccharides in breast milk that are beneficial for the microbial community in their gut.

As we learn more about the connection of the infant gut microbiome with breastfeeding, it's likely that current recommendations to breastfeed will become even stronger. The World Health Organization currently recommends exclusive breastfeeding for at least the first 6 months of life.

However, if you feed your baby formula, know that formula provides a healthy diet for your infant as well. Some formulas are fortified with probiotics, oligosaccharides, and other beneficial ingredients that mimic those found naturally in breast milk.

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Verywell Family uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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Additional Reading
  • Kliegman, Robert M., Bonita Stanton, St Geme III Joseph W., Nina Felice. Schor, Richard E. Behrman, and Waldo E. Nelson. Nelson Textbook of Pediatrics. 20th Edition. Philadelphia, PA: Elsevier, 2015. Print.

By Cara Henderson
Cara Henderson is a registered dietitian nutritionist. Her writing and editing experience includes serving on the editorial board of Preemie magazine, and 17 years of experience writing for health and wellness publications.