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Lupus and the Gastrointestinal System

Lupus is a systemic inflammatory disease that, if left untreated, can affect virtually any body part. Though it is known to most commonly affect the kidneys, lungs, brain, heart and joints, the gastrointestinal system is not exempt from its clutch. People with lupus often experience problems with the GI system/tract and can even have issues with the surrounding organs.

The gastrointestinal tract is a part of the digestive system, consisting of the liver, gallbladder, and pancreas. It is a complex pathway of connected hollow organs, including the mouth, esophagus, stomach, small intestine, large intestine, and anus. Its main job is to break down food into the energy and nutrients that are needed to survive and expel the rest as solid waste. Since food contains a balance of proteins, carbohydrates, fats, minerals, and vitamins, this process is essential because the body needs food and liquids to stay healthy and grow. In a nutshell, the GI system/tract is the body’s doorway for bringing in, breaking down, and disposing of everything. The GI tract needs to function well to absorb nutrients from food and liquids properly, repair cells, and supply energy.

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The GI system is divided into two parts: upper and lower. The upper GI system comprises the buccal cavity, pharynx, esophagus, stomach and duodenum. The lower GI tract includes the small intestine (duodenum, jejunum, and ileum) and the large intestine (cecum, colon, rectum and anal canal). Many parts of the upper and lower digestive system can be affected by lupus inflammation. Not only that, medications prescribed to treat SLE and other overlapping conditions may cause issues with it as well. This blog will discuss some of the most common problems with lupus and the gastrointestinal system.

Lupus and the Esophagus:

Stomach acid can back up into your esophagus (a muscular tube that sits behind the trachea) and cause discomfort. This backward flow of acid, called reflux, can be expected from time to time and experienced by anyone. However, when it is a persistent issue that causes pain and discomfort, it is known as gastroesophageal reflux disease (GERD). Causes for GERD include Hiatal hernias, weak sphincter muscles or weak contractions in the esophagus. Treatment for GERD includes over-the-counter quick acting medications that control acid (Maalox®, Mylanta®, Rolaids® and Tums®). Other medicines called H-2 receptor blockers (Pepcid AC®, Tagamet HB®) are used to help long term. Surgery to reinforce the lower esophageal muscles may also be an option if medications do not provide symptom relief.

Here are some tips to help with heartburn/GERD from Dr. Thomas and his handbook, The Lupus Encyclopedia (p. 257):

  • Eat smaller, more frequent meals

  • Take smaller bites

  • Elevate the head of the bed while resting or sleeping and do not lie down as least two hours after eating

  • Avoid excessive caffeine, tobacco, chocolate, high-fat foods, and alcohol.

  • Promote saliva formation (especially if you have Sjogren’s Syndrome) by using sugar-free gum and candies

As mentioned, this can happen to anyone, but lupus can cause an increase of inflammation in the esophagus and weaken the muscles used to swallow. It is believed that roughly 25% of lupus patients will develop a problem with the esophagus muscles, called esophageal dysmotility. This condition can cause issues with swallowing, heartburn, and even chest pain. This disorder is treated similarly to GERD; however, steroids are sometimes helpful if the problem is due to systemic lupus inflammation.


Though digestive problems seem to be common in lupus (50% of patients with SLE say they have them), there has been difficulty in identifying the exact causes why. It is pretty perplexing considering Crohn’s and colitis (see below) are rare to coincide with SLE and celiac disease (an autoimmune disorder related to gluten sensitivity believed only to affect 2.4% of SLE patients). However, symptoms such as vomiting, nausea, diarrhea, and constipation all make the top of the “digestion frustration'' list for many SLE patients. One possibly may be due to the GI muscles not moving waste through the intestines properly. Another might be Irritable Bowel Syndrome or (IBS).

IBS is a disorder that affects the colon and causes cramping, abdominal pain, bloating, gas, diarrhea and constipation. IBS is considered a chronic condition and is believed to be related to irregularities in the nervous system. In mild cases, IBS can be controlled by lifestyle changes, including avoiding trigger foods, exercising, managing stress, drinking plenty of water, and getting proper sleep. Finding the right balance of healthy foods can be a challenge with IBS; however, some doctors have found having their patients on the low FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) diet has helped reduce gassiness, abdominal pain, and bloating in their patients.

Working with a dietician is recommended to ensure patients are still getting all the nutrients they need, no matter the diet. In more moderate to severe cases, smooth muscle relaxants, antidiarrheal, laxatives, and even antibiotics have been found helpful for symptom management.

A somewhat rare complication with lupus called protein-losing enteropathy can also cause digestive woes. (PLE) has been associated with more than 60 different conditions, including nearly all gastrointestinal diseases. Symptoms include diarrhea, feeding intolerance (unable to eat or digest food without getting sick) and edema (fluid retention or swelling, particularly in the extremities). If this is the case, patients struggle with absorbing protein and need to see a specialist to determine the right treatment.

I would be remiss if I didn’t mention Sjögren’s disease in this section because it can affect digestion. Sjögren's (SHOW-grins) disease is a disorder of your immune system identified by its two most common symptoms — dry eyes and a dry mouth. A dry mouth can cause issues with breaking down and swallowing food. The lack of saliva also can cause bacteria to build in the mouth, causing cavities and dental decay, as well as heartburn, reflux, and esophagitis. It can worsen GERD and cause constipation as well.

Inflammatory Bowel Disease:

Inflammatory Bowel Disease is an umbrella term for many conditions that cause inflammation of the intestine and colon. Crohn’s disease and Ulcerative colitis are two examples of inflammatory bowel disease. Crohn's is an ongoing disease associated with inflammation of the GI tract that can cause bloody diarrhea and abdominal pain. It can be tricky to tell the difference between the two because Colitis can also cause similar symptoms. Ulcerative Colitis differs from Crohn's disease mainly because it only affects the large intestine's innermost lining, and the inflammation (or ulcers) is usually only found in the rectum and parts of the colon. People with lupus may develop ulcerative colitis, but it appears rare for someone to have both lupus and Crohn’s disease.

Many doctors are unsure if lupus inflammation is the cause of inflammatory bowel disease. However, there does seem to be more evidence suggesting some immune deregulation commonalities between the diseases. Treatments for Crohn's disease include medications (antibiotics, aminosalicylates, corticosteroids, immunomodulators and biologics) and surgery (strictureplasty, resection and proctocolectomy or colectomy). Treatments for ulcerative colitis include medications (aminosalicylates, corticosteroids, immunomodulators and biologics), and surgery (colectomy) to have an internal or external waste bag attached to their abdominal wall.

Peptic Ulcers:

Sadly, some lupus medications can add to the potential development of GI issues. Certain medications (like NSAIDs) may increase the risk of developing ulcers (a fancy word for hole) in the stomach lining and duodenum. A peptic ulcer occurs when stomach acid erodes through the lining of the esophagus, stomach, or part of the small intestine. Peptic ulcers can cause a burning, gnawing, painfully "hunger-like” discomfort. Gastric ulcers worsen with eating; however, duodenal ulcers usually do not. There can be a range of complications from ulcers, and if one is suspected, it is essential to seek medical care right away due to the risk of bleeding. A bleeding ulcer left untreated can be very dangerous.

Also, certain bacteria like Helicobacter pylori (pronounced Hel-ee-Koh-BAK-her Pie-LORE-ee) that infect the stomach also cause ulcers and can be more common in people with lupus due to generally having higher risks of infection. However, having H. pylori is common, particularly in Hispanic and LatinX ethnicities. Most people who have it won’t get ulcers or show any symptoms; however, when it becomes problematic, it is treated with PPI medications like Prevacid®, and Prilosec® and antibiotics to kill the bacteria.


Inflammation of the pancreas is known as pancreatitis. This condition may be caused by lupus, by vasculitis (inflammation of the blood vessels in the pancreas), and by certain medications. Corticosteroids, immunosuppressants, and diuretics have been known to occasionally cause pancreatitis. Other more common causes include gallbladder stones and excessive alcohol intake. Though pancreatitis from SLE is on the rarer side, it can be dangerous, especially in children. Lupus-related pancreatitis is treated with high doses of steroids and azathioprine (I know, ironic, right?). People are usually told to stop eating and drinking for a period to allow the pancreas to heal. Treatment also includes hospitalization, IV fluids, and rest.


Inflammation of the peritoneum (the thin lining of the abdomen) is called peritonitis. Sometimes people living with SLE can experience peritonitis because of fluids that build up in the abdominal cavity (ascites). It is rarely diagnosed, but has been found to be more common than realized. The symptoms experienced from peritonitis include severe abdominal pain, belly tenderness, nausea/vomiting, fever, and lack of bowel movements. Proper diagnosis is crucial because many things can cause peritonitis and the symptoms can mimic other disorders. Doctors may take a sample of the fluid from the belly to confirm the diagnosis and determine the proper treatment.

The Liver:

The liver is one of the most important (and the largest) organs inside the body and has many responsibilities. The liver makes bile (a bitter alkaline fluid that aids in digestion), changes food into energy, and cleans poisons from the blood. Lupus inflammation in the liver can cause many issues, including hepatic vasculitis and blood clots. If antiphospholipid antibodies are present, this may increase the occurrence of blood clots in the vessels of the liver. Lupus patients can experience increased enzyme levels from disease activity or from taking NSAIDs and acetaminophen. This results in the development of jaundice, which is a yellowing of the skin and whites of the eyes.

Another liver complication is autoimmune hepatitis. Autoimmune hepatitis is classified into two categories: type 1 or 2. Type 1 is the most common and can occur at any age. 50% of individuals with type 1 have another autoimmune disease, like lupus, Sjögren's syndrome, type 1 diabetes, or ulcerative colitis. Type 2 is less common and typically only affects females between the ages of 2 to 14. Symptoms of autoimmune hepatitis include fatigue, enlarged liver, jaundice, abdominal pain, nausea and vomiting, itching and skin rashes, joint pain, dark urines, abnormal blood vessels on the skin, loss of appetite, and pale or gray-colored stools.

People can experience forms of viral and drug-induced hepatitis as well. It is vital to disclose to a physician all prescription and over-the-counter medications to receive proper diagnosis and treatment. Autoimmune hepatitis is treated with corticosteroids and sometimes immunomodulators like azathioprine.

The Problems with Prescriptions:

Gastrointestinal symptoms are common in SLE patients, and unfortunately, some issues are caused by the medications used to treat lupus. Taking steroids, non-steroidal anti-inflammatory drugs, calcium channel blockers (for Raynaud’s, antidepressants, bisphosphonates (for osteoporosis), and pain relievers can impact digestive health.

People need to weigh the pros and cons of every medication to ensure they are helping their lupus symptoms more than they may be hurting the GI system. However, NEVER stop taking a medication without first discussing with your doctor.

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Lupus and the Microbiome:

The gut microbiome is an assembly of microorganisms (such as bacteria, viruses, etc.) that live in the human digestive tract. Recent research has found the microbiome plays a role in developing and regulating the immune system. Several recent studies have suggested that alterations in the gut microbial composition may correlate with lupus disease manifestations. The studies provided examples of those with lupus having a decrease in beneficial bacteria and an increase in harmful ones. They also found medications played a role in the variety and level of gut bacteria. Additionally, people with lupus who have been on high doses of glucocorticoids (steroids) were more likely to have disturbances in the makeup of their gut microbiomes.

While more research is needed to fully understand the relationship between lupus and the gut microbiome, it is exciting to think that there is a future where possibly something as simple as altering a diet to improve gut microbiome may be a treatment for lupus symptoms.


Lupus can affect the GI system, but it doesn’t mean it will. However, if you encounter GI issues, don’t be embarrassed to tell your doctor immediately. A special doctor called a gastroenterologist can work with your rheumatologist to find a treatment plan that works for you.

Remember to always listen to your gut. There is no one who knows you better than YOU!

Written By: Kelli Roseta

Reviewed by: Donald Thomas, M.D., FACP. FACR, RhMSUS

**All resources provided by this blog are for informational purposes only, not to replace the advice of a medical professional. Kelli encourages you to always contact your medical provider with any specific questions or concerns regarding your illness. All intellectual property and content on this site and in this blog is owned by This includes materials protected by copyright, trademark, or patent laws. Copyright, More Than Lupus 2022.


The Lupus Encyclopedia, Dr. Donald Thomas, Jr. MD., FACP, FACR, Johns Hopkins Press, 2014, pages 254-264

Medically reviewed by Dr. Don Thomas

December 2022

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