Understanding Small Intestine Problems

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The small intestine, also called the small bowel, is part of the digestive tract. This organ connects the stomach and the large intestine and is the longest part of the digestive system.

As food being digested travels through it, the small intestine absorbs vitamins and minerals. Problems with the small intestine can cause not only discomfort but also nutritional problems, and this can affect the rest of the body.

Diseases and conditions that can affect the small intestine include Crohn’s disease, celiac disease, small intestinal bacterial overgrowth (SIBO), and irritable bowel syndrome (IBS). This article will provide a brief overview of some of the more common small bowel disorders, including symptoms, causes, diagnosis, and treatment.

Common Symptoms of Small Intestine Problems

Verywell / Jessica Olah

Conditions That Affect the Small Intestine

When food is chewed and swallowed, it goes down the esophagus (food tube) into the stomach, and then into the small intestine. It travels through the three parts of the small intestine—the duodenum, jejunum, and ileum. The muscles in the walls of the small bowel move the food along while it is digested and vitamins and minerals are absorbed.

Several problems can occur in the small intestine and affect how well it digests food. 

Crohn’s Disease 

Crohn’s disease is one form of inflammatory bowel disease (IBD). It can affect the small intestine as well as the rest of the digestive tract. It causes inflammation in the lining of the walls of the gut. This can lead to ulcers. Other problems that can occur in the digestive tract include pain, diarrhea, constipation, and not digesting food well. 

Outside of the gut, there can also be problems with the eyes, skin, and joints. Crohn’s disease attacks the digestive system, but it can also affect the whole person in various ways.

Celiac Disease

Celiac disease is an autoimmune disease, a condition in which the immune system mistakenly attacks a person's own body. Celiac disease affects the small intestine. The lining of the small bowel is covered in villi, which are like little fingers. The villi absorb nutrients from food.

When a person with celiac disease eats gluten, white blood cells attack the villi, which then become worn down. This leaves the small intestine less able to absorb vitamins and minerals from food.  

Some people may experience no symptoms, but for those who do, symptoms include diarrhea or constipation, bloating, abdominal pain, vomiting, weight loss, and fatigue. There can also be signs in other parts of the body that include anemia (lack of healthy red blood cells), joint pain, or other problems, especially in adults.

Irritable Bowel Syndrome

IBS is a common condition that can affect the intestines. It can cause constipation, diarrhea, abdominal pain, bloating, and other signs and symptoms. The symptoms can be bad enough to interfere with daily life, such as going to school or work and socializing.


A small intestine obstruction or blockage means that there is something blocking food from going through. This can happen as a result of another condition, such as Crohn’s disease. Inflammation can cause the bowel to become blocked or lead to scar tissue that thickens the walls of the intestine.

Food can become stuck if there is a condition that causes the small bowel to move food too slowly (called motility disorders). A bowel obstruction can be an emergency. Blockages might be treated with medication and fluids in the hospital. In serious cases, surgery might be needed.

Small Intestine Bacterial Overgrowth

The small and large intestines are normally home to microorganisms (gut flora), which are essential to their function. The bacteria can get out of balance and overgrow. This can lead to symptoms such as gas, bloating, constipation, or diarrhea, as well as weight loss or other symptoms outside the digestive system.

SIBO can be difficult to diagnose and treat. It might be associated with other conditions such as IBS, diabetes, or autoimmune conditions.

What Are the Symptoms of Small Intestine Problems?

In some cases, a problem with the small intestine might not cause any symptoms at all. Signs and symptoms will depend on which disorder is causing the problem, but there are some that may be more common across conditions.

These can include:

  • Abdominal bloating
  • Abdominal pain or discomfort
  • Constipation
  • Diarrhea
  • Gas
  • Nausea
  • Vomiting

What Causes Small Intestine Problems?

The causes of small intestine problems are different based on the condition. In some cases, the causes might not be well understood and include:

  • Celiac disease: Celiac disease is thought to be genetic, but only certain people who have the genes for the disease go on to develop it. Environmental triggers may cause people to develop the disease.
  • Crohn’s disease: The causes aren’t known, but it’s thought to be a complex combination of genetics and one or more triggers in the environment.
  • SIBO: The change in bacteria is thought to potentially be caused by slow motility (decreased movement), low levels of stomach acid, or having surgery on the small bowel.
  • Obstruction: An obstruction is caused by a narrowing of the small intestine or from either food or a foreign object being stuck. This can be due to a disease that causes inflammation or scar tissue or from slow motility in the bowels.

How Are Small Intestine Problems Diagnosed?

When problems in the small intestine start, the signs and symptoms might not seem related to digestion. In some cases, it might take time and a healthcare provider who is good at diagnosing to get to the heart of the matter.

Some of the tests that might be used to find problems in the small intestine include: 

  • Barium swallow and small bowel follow-through: In this test, X-rays are taken after drinking a contrast solution (barium) to see the esophagus, stomach, and small intestine.
  • Blood tests: Blood tests won’t be used to make a diagnosis, but they can find problems such as anemia or vitamin deficiencies. 
  • Colonoscopy: A colonoscopy is used to find problems with the colon (large intestine) rather than the small intestine, but this test might be used to rule out other digestive conditions.
  • Computed tomography (CT) scan: This is a type of X-ray that takes detailed images of internal organs in the abdomen.
  • Magnetic resonance imaging (MRI): This test uses a strong magnet to scan the abdomen and provide images.
  • Endoscopy: A small tube with a light and camera on the end is inserted into the mouth and down the esophagus to the stomach and the first part of the small intestine. A biopsy (a piece of tissue or fluid) might be removed to be tested.
  • Breath testing: A breath test may diagnose or rule out small intestine bacterial overgrowth.
  • Stool tests: To rule out problems like an infection, stool might be sent to a lab for testing, which may include a bacterial culture.
  • Ultrasound: This test uses sound waves to see the organs and structures in the abdomen.

How Are Small Intestine Problems Treated?

The treatment for small bowel conditions will be different based on what’s causing them. However, part of treatment might include lifestyle changes such as nutrition and diet, stress reduction, or working with a mental health professional.

The treatment for celiac disease is avoiding gluten. There currently aren’t any medications to treat the condition, although there may be treatments for symptoms outside the digestive system.

Crohn’s disease is treated with lifestyle changes as well as medications. In some cases, such as when the bowel becomes narrowed, surgery might be needed. 

IBS may be treated with lifestyle changes, diet and nutrition, and medications. People with IBS may also work towards controlling symptoms by identifying what environmental triggers may set them off. 

SIBO may be treated with antibiotics to curtail the growth of the bacteria. Other treatments could include getting any associated conditions under control, as well as nutritional support.

Bowel blockages might be treated in the hospital with decompression, which is done by inserting a flexible tube through the nose and down into the stomach. In some cases, surgery to remove the blocked section of the small intestine might be needed.


Diseases and disorders of the small intestine are common. They include Crohn’s disease, celiac disease, small intestinal bacterial overgrowth, and irritable bowel syndrome. These may cause digestive symptoms such as abdominal pain, bloating, diarrhea, constipation, nausea, or vomiting. They may also lead to vitamin deficiencies or anemia.

Diagnosis of these conditions may take time and a variety of imaging tests. Treatment may involve making changes to lifestyle, especially to diet. For some conditions, medications and surgery might also be used to manage the signs and symptoms.

A Word From Verywell

Small intestinal problems can be tricky to diagnose and treat. It may help to get a referral to a gastroenterologist (a doctor who specializes in the digestive system). Sometimes small intestine problems cause signs and symptoms outside the digestive system so it can take time to find the problem.

When the small intestine is causing nutrients to not be absorbed properly, you can have problems throughout the body. It can take self-advocacy to get small intestine problems diagnosed and treated. Asking questions and pushing for answers may be part of the process to get a diagnosis and proper treatment.  

Frequently Asked Questions

  • What causes bowel disorders?

    In many cases, the causes of bowel diseases are not well understood. Sometimes there is a genetic reason that makes people more likely to develop a bowel disorder. Often there is also one or more environmental triggers that “turns on” the disease. People might not know that they have the possibility of developing a bowel problem until the symptoms start.

  • Can small intestine problems cause cancer?

    Cancer in the small intestine is rare. Most diseases of the small intestine don’t lead to a risk of cancer. However, celiac disease and Crohn’s disease are both associated with a slightly increased risk of small bowel cancer. A doctor can help you understand the risk of cancer.

  • What conditions can affect the small intestine?

    The common conditions that can affect the small intestine include Crohn’s disease, celiac disease, bowel obstructions, small bacterial overgrowth, and irritable bowel syndrome. Other, more rare conditions can also affect the small bowel, such as cancer.

    Talking to a healthcare provider about your risk of small bowel problems can help your understand if you have a chance of developing them.

8 Sources
Verywell Health 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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By Amber J. Tresca
Amber J. Tresca is a freelance writer and speaker who covers digestive conditions, including IBD. She was diagnosed with ulcerative colitis at age 16.