GI Tract: Structure

Mar 5, 2017 by

You can have me read this article to you instead of reading it yourself…

Or you can read it the old-fashioned way below…

Understanding the structure of the GI tract is crucial for fully understanding how this part of the body works.  Which leads to understanding what happens when it stops working.

As I mentioned in the section on GI tract function, structure and function go hand in hand.  So you will notice that while this section might be built around discussing structure, I actually spend at least as much time discussing function.

For the sake of making this information more digestible (ha…ha), I am splitting the GI tract into the segments of upper and lower.  But please refer to the lovely illustration below as often as needed.  This was created just for us in order to cover this topic (thank you, Randy)!

GI Tract Structure Illustration

The Structure and Sequence of the GI Tract


Upper GI Tract


The mouth is where digestion begins, starting with chemical breakdown from saliva and mechanical breakdown from chewing. There are also some nutrients and medications that are partially absorbed in the mouth.  For this reason, you will sometimes see orally disintegrating tablets or sublingual tablets.

After chemical and mechanical digestion, everything exits the mouth quite rapidly and enters into the…


The esophagus is easily described as a tube that connects your mouth to your stomach.  But that’s a much too simple description.  This tube is still made up of muscle and nerve tissue, and marks the start of something called peristalsis.

Peristalsis is a movement that is made up of involuntary contractions.  In other words, muscles in your GI tract are supposed to constantly move in a sequence that pushes food down the esophagus and into the stomach. Once in the stomach, peristalsis causes the stomach to move around and perform mechanical digestion.  The same peristalsis is active in the intestine, where it continues to be responsible for pushing food in the right direction.

There are a number of things that can go wrong with peristalsis.  Unregulated movement might cause the food to get stuck or move in the wrong direction.  A complete lack of peristalsis, which means that there is no movement at all, can cause significant delays in the movement and digestion of foods.  Those with gastroparesis will recognize this as the hallmark of their condition.

Esophageal Sphincter

The gateway between the esophagus and the stomach is called the esophageal sphincter. This is a flap that keeps the food moving in only one direction: esophagus to stomach.

When there is a vomiting reflex, it overrides this sphincter and pushes food back into the esophagus.  Other issues can also occur with this sphincter.  Due to certain foods or medications, it can become loose.  This allows food to leak past it in the wrong direction.  For others, the sphincter can become completely ineffective, which leaves an opening for food to move in both directions relatively freely.

It is possible for many people with gastroparesis to experience regurgitation (without a vomiting reflex). This likely means that they have some type of esophageal sphincter malfunction.  And many people with IBS and IBD experience GERD (or acid reflux), which may also indicate an issue with this sphincter.


Mechanical and chemical digestion both occur inside of the stomach.  This happens through movement of the stomach as well as through the presence of stomach acid.

There is a distinct difference between the acid that is produced by the stomach on a regular basis and the acids that come from the food that has been eaten.  This is important to recognize if you are experiencing acid reflux.  The medications that are taken every day to treat acid reflux work by stopping stomach acid production.  Antacids, on the other hand, work by binding the acid that is already in the stomach.  As you can imagine, this means that each situation may be better treated with a different set of options.

My book, Gastroparesis: A Roadmap for Your Journey, contains an entire chapter on the topic of acid reflux and the considerations to make in order to manage it well.  The full chapter is available for free on the linked page if you are interested in learning more on this topic.

The stomach is not as relevant to those with IBD and IBS as it is to people with gastroparesis, so I go into much more detail in that section.  From here, the food moves through the…

Pyloric Sphincter

Once the food is adequately broken down to a liquid form, it drains out of the stomach through the pyloric sphincter. Just as with the last sphincter, this one also works to keep the contents of the GI tract moving in only one direction: stomach to small intestine.

This sphincter does not suffer from the issues that are seen with the esophageal sphincter nearly as often.  However, it is possible for the contents of the small intestine to push back up into the stomach.  This is unusual, and happens far less often than the experience of acid reflux.  When the food exits the stomach, it mixes with other ingredients to form bile.  That is why something is referred to as ‘bilious’ when it pushes upwards from the small intestine.

Lower GI Tract

The lower GI tract refers to the intestine, which is made up two major segments – the small intestine and the large intestine (see the illustration above).  The small intestine is broken down further into three pieces, called the duodenum, jejunum, and ileum.


From the pyloric sphincter, the food enters the duodenum. The nutrients in the food are now broken down by enzymes, allowing them to be absorbed and used by the body.  The duodenum is only the beginning of this breakdown and absorption, which continues throughout the small intestine.  But the enzymes are highly concentrated in the duodenum due to the…


Enzymes for nutrient breakdown come from the pancreas and are referred to, understandably, as pancreatic enzymes. The primary components here are enzymes that break down fats, proteins, and carbohydrates (sugars). Additional enzymes break down fibers and other nutrients that may be difficult to digest.

All pancreatic enzymes are delivered to the duodenum and mixed with the digested food that has exited the stomach. Something called sodium bicarbonate is also released from the pancreas into the duodenum. This chemical deactivates the acid that was mixed with the food while in the stomach.

This is a departure from the other parts of the GI tract because our food does not actually pass through the pancreas. However, I’ve included it here because this organ is crucial to the function of the GI tract and feeds directly into the small intestine. The pancreas is more well-known for its role in diabetes and producing insulin.


From the duodenum, the food moves into the next section of the small intestine – the jejunum. The jejunum’s primary function is the absorption of the nutrients in the food. It is full of cells that are made to pull nutrients into the body.

The jejunum is also an important place for absorbing water into the body.  The ultimate goal here is to leave nothing valuable in the intestine – it should only end up with indigestible and nutrient-free waste.  Once nutrients are absorbed they are typically processed by the liver, but we will not discuss this processing in any detail here.


After the jejunum, the food passes into the next part of the intestine called the ileum. The ileum basically acts as the cleanup for nutrient and water absorption.  It picks up anything that was not absorbed by the jejunum, and is responsible for absorbing specific nutrients that the jejunum cannot absorb.

Keep in mind that peristalsis is active in the intestine as well as in the esophagus and stomach.  Muscle contractions are responsible for keeping food and stool moving towards the rectum all the way through the intestine.  Some people may have a change in peristalsis in the upper GI tract, but not the lower GI tract, and vice versa.  A change in peristalsis can cause very different symptoms when it occurs in different locations.

The end of the ileum is called the terminal ileum.   This marks the gateway between the small intestine and the large intestine.  This is of particular importance for those with IBD, which I discuss much more in that section.

Large Intestine (Colon)

After completing its run through the small intestine, the contents are moved into the large intestine through a passage called the cecum.  The terms large intestine and colon are often used interchangeably.

This portion of the intestine is also responsible for absorbing the last bits of nutrients and any extra water. Certain vitamins are produced by the bacteria found in the colon, and are absorbed from this location (such as Vitamin K, Vitamin B12, Vitamin B1 or thiamine, and Vitamin B2 or riboflavin).


Finally, the food makes its way to the rectum, where it is stored until it exits the body through the anus. And as we are all aware, stool can come in many forms, from fully liquid to very hard and solid.  There are many causes for these changes in its form.

This is also the location for the development of hemorrhoids, which can be a source of discomfort and even bleeding for many people with IBS.  We discuss this concept further in that section.

With that, we have now run the length of the GI tract.  I’d say it’s time to talk about what’s living inside of it…

Next: Bacteria and the Gut

Or refer back to the GI Tract Info Hub.

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