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Autoimmune Gastritis: What Is It, Could You Have It and How Is It Treated?

Your Guide to the Causes, Symptoms, Diagnosis and Treatment of Autoimmune Gastritis

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Nausea, a sore stomach, fatigue, and pins and needles. While these may seem like vague and varied symptoms, they can all be the result of a chronic inflammatory condition of the stomach known as autoimmune gastritis.

Figures suggest around 2% of the U.S. general population, or around one in 50 people, has autoimmune gastritis [1].

Having a pre-existing autoimmune disorder, such as a thyroiditis, vitiligo, Addison’s disease, or type-1 diabetes makes you much more prone to the condition.

In this article, I’ll walk you through some of the signs and symptoms of autoimmune gastritis as well as its diagnosis, risk factors and treatment options, including diet, probiotics, and vitamin B12. We’ll also touch on how autoimmune gastritis overlaps with several other autoimmune conditions.

autoimmune gastritis: Autoimmune disease written in a notebook surrounded by different things

What Is Autoimmune Gastritis?

“Gastritis” refers to inflammation in the gastric region (stomach), while “autoimmune” refers to the fact that this condition is caused by the body’s immune system attacking its own body cells.

Other terms for autoimmune gastritis include “autoimmune metaplastic atrophic gastritis,” “chronic autoimmune atrophic gastritis,” or combinations of these terms.

Autoimmune gastritis is a specific type of atrophic gastritis. Atrophic gastritis — or chronic stomach inflammation — is common: Estimates suggest that around a quarter of the population may have this chronic condition [2].

As the name suggests, atrophic gastritis or chronic atrophic gastritis involves atrophy (wasting away) of a part of the stomach lining known as the oxyntic mucosa. This includes a destruction of the parietal cells (oxyntic cells) that produce stomach acid as well as the substance known as intrinsic factor, which is essential for vitamin B12 absorption. It also includes destruction of cells that produce the main digestive enzyme pepsin in the stomach.

As the condition progresses, some of the normal stomach lining cells get replaced with abnormal intestinal-type cells (so called intestinal metaplasia). Intestinal metaplasia is recognized as a precancerous lesion, putting those affected at a six times increased risk of getting a common gastric cancer called gastric adenocarcinoma [3]. So getting diagnosed and treated for atrophic gastritis as soon as possible is key.

What Causes Autoimmune Gastritis?

Autoimmune gastritis is one of as many as 100 autoimmune conditions that are becoming more common. Rheumatoid arthritis, Hashimoto’s thyroiditis and inflammatory bowel disease are other examples [4]. 

Evidence suggests that increased permeability of the intestine or a “leaky gut”— driven by gut dysbiosis (disruptions to the healthy balance of bacteria in the gut) [5] — may behind many of these autoimmune conditions [6, 7, 8, 9, 10, 11, 12, 13].

Food intolerances that can occur as a result of gut imbalances [14, 15, 16, 17, 18, 19] can further drive autoimmune conditions, creating something of a vicious circle. With a leaky gut, food particles that aren’t fully digested leak into your bloodstream. So, the immune system may view them as potential threats and initiate an inflammatory response, further exacerbating your autoimmune condition.

Atrophic Gastritis vs. Autoimmune Gastritis

autoimmune gastritis: Illustration of a healthy gastric mucosa vs a gastric mucosa with atrophic gastritis

Though in both cases there is atrophy of the stomach’s mucosal lining, what distinguishes chronic autoimmune gastritis from more general atrophic gastritis is the underlying cause:

  • Atrophic Gastritis: Atrophic gastric is generally caused by a Helicobacter pylori infection [20] — this bacterium can survive in the high acidity of the gastric mucosa. Over time, this creates chronic inflammation.
  • Autoimmune Gastritis: In the case of autoimmune gastritis, the damage to the gastric mucosa is caused by a malfunctioning immune system, which may be caused by a combination of genetic factors and those relating to gut bacteria disruptions discussed above [1].

There may, however, be a link between H. pylori infection and autoimmunity — one theory is that the bacterium sets off the immunological processes that can lead to autoimmune gastritis [21]. Other research indicates up to 30% of people with H. pylori infection also have autoantibodies to parietal cells, and these disappear when the infection is eradicated [22].

Can Reflux Medications Cause Atrophic Gastritis?

autoimmune gastritis: Omeprazole capsules with a plastic medicine bottle

Proton pump inhibitors (PPI) — drugs such as omeprazole that are given to help with GERD and acid reflux — have been touted as a potential increased risk for atrophic gastritis (though not autoimmune gastritis specifically).

For example, a 2017 systematic review and meta analysis found moderate evidence that incidence of gastric atrophy was statistically higher in those taking PPIs [23]. But it’s certainly not clear-cut — another systematic review and meta analysis in 2014 found no compelling evidence that long-term PPI use caused or accelerated gastric atrophy or intestinal metaplasia [24].

Whatever the main underlying cause of your stomach inflammation, many of the health issues you can experience are a result of reduced stomach acid secretion. 

Signs and Symptoms of Autoimmune Gastritis

Autoimmune Gastritis: What Is It, Could You Have It and How Is It Treated? - Symptoms of Atrophic Gastritis Square L

It’s possible to have chronic atrophic gastritis or autoimmune gastritis and not realize it. In fact, it’s really common for the condition to be quite advanced before it is recognized. But non-specific symptoms like fatigue, bloating, and abdominal pain may be signs of gastritis. Identifying the cause as early as possible can help you to feel better and avoid more serious complications. Autoimmune gastritis usually moves from mild to severe within three years [22].

When you do experience symptoms, these may include [25]:

  • Nausea and vomiting
  • Feeling full in the upper abdomen after eating
  • Abdominal pain
  • Fatigue

You might feel pain and discomfort specifically in the upper (fundus) part of the stomach because it’s where the acid-secreting parietal or oxyntic cells are concentrated. 

In autoimmune gastritis, the immune system attacks the acid-producing machinery known as the H+/K+ ATPase proton pump inside the parietal cell.

Low Stomach Acid

autoimmune gastritis: Risk factors for low stomach acid chart by Dr. Ruscio

Many of the signs and symptoms of atrophic gastritis — whether autoimmune in nature or not — actually occur because of a lack of stomach acid secretion (also known as achlorhydria).

What happens when your stomach acid production is low? For a start, you will be less able to fight off gastrointestinal infections, and you may also experience digestive problems and much poorer absorption of some nutrients.

Malabsorption of nutrients, particularly vitamin B12, is one reason why many people with achlorhydria and advanced autoimmune gastritis may experience [26]: 

  • Extreme fatigue
  • Nervous symptoms like numbness and tingling
  • Increased risk of heart disease

Chronic achlorhydria can also lead to increased risk of stomach cancer — in this case, a slower growing carcinoid tumour [27].

The sequence of events goes like this:

Low stomach acid —> excess gastrin hormone produced by the lower antrum region of the stomach in an attempt to restore acid levels —> overgrowth (hyperplasia) of “enterochromaffin-like” cells in the stomach lining —> development of gastric carcinoids

Pernicious Anaemia

Stressed woman with her hand on her forehead and her eyes closed while working

Pernicious anaemia related to a lack of stomach acid and intrinsic factor is one of the main longer term conditions that can result from autoimmune gastritis [28].

In pernicious anaemia (also known as megaloblastic anemia), red blood cells don’t divide properly and are too large and too few in number. The symptoms can be serious [29] – including not just debilitating fatigue and an inability to concentrate, but also nervous system damage that can start as pins, needles and numbness, and can progress to irreversible neurological damage. 

Supplementing to overcome a vitamin B12 deficiency is therefore key to treating autoimmune gastritis, which we’ll talk about more in the treatment section below.

How Is Autoimmune Gastritis Diagnosed?

Often, autoimmune gastritis is not diagnosed until after antibiotic treatment for eradication of a suspected Helicobacter pylori infection has been ineffective or only partially effective.

A definitive diagnosis of autoimmune gastritis can usually be made by a specialist in gastroenterology after an endoscopic biopsy. In this procedure, a doctor inserts a flexible thin tube (an endoscope) with a tiny camera and light down into your stomach and collects a small sample of tissue.

Is Antibody Testing Helpful?

The anti-parietal cell antibody test (also known as the parietal cell antibody test) is another potentially useful test that is less invasive than endoscopy. 

This blood test checks for the presence of autoantibodies that are suggestive of autoimmune gastritis. 

However, I would always use this test on a case-by-case basis because it isn’t specific — parietal cell antibodies can also be found in atrophic gastritis and can be a hallmark of autoimmune thyroid disease and type-1 diabetes. 

Parietal cell antibodies may also only be elevated earlier in the disease and can sometimes fall again as the disease progresses and the oxyntic mucosa continues to deteriorate, so the results may be confusing or misleading [1, 22].

Other tests that may or may not be relevant depending on your own condition include:

  1. Anti-intrinsic factor antibody test — more specific than the antiparietal cell antibody test for detecting pernicious anemia
  2. Anti-H. pylori antibody test — for when H. pylori infection is also suspected
  3. Gastrin-17 test — helps identify deterioration of the oxyntic mucosa (gastrin is the hormone that stimulates stomach acid secretion)
  4. Pepsinogen I and pepsinogen I / Pepsinogen II serological tests — effective screens for advanced atrophic gastritis (pepsinogen is the precursor to the digestive enzyme pepsin)

Related Diagnoses (and the Gut-Bacteria Connection)

autoimmune gastritis: Gut-bacteria connection chart

Autoimmune conditions often come in clusters. If I see someone with a diagnosis of autoimmune gastritis, I would almost certainly expect them to have related autoimmune disease.

In fact, a 2012 observational study found more than half of a group of 99 patients with autoimmune gastritis had other autoimmune conditions, including Hashimoto’s thyroiditis, type-1 diabetes, vitiligo, celiac disease, rheumatoid arthritis, Grave’s disease, connective tissue disease, and psoriasis [30].

A common thread that ties all these autoimmune conditions together is your gut microbiome. Across many autoimmune diseases, there is often shared disruption to the healthy balance of bacteria in the gut [31].

That’s why it’s vitally important to look at your symptoms as a whole. We’ll run through a series of recommended treatment steps in the next section that will help with autoimmune diseases in general as well as autoimmune gastritis more specifically. While these generalized treatments might help, an expert in functional medicine is uniquely qualified to help look at all your symptoms and the underlying causes holistically, should you need extra help.

Treating Autoimmune Gastritis

Many of the treatments that may help with autoimmune gastritis also help autoimmune disease generally.

Dietary Measures

I really can’t overstress how helpful dietary changes can be in tackling autoimmune conditions and improving your gut health, which underlies so many aspects of our health.

To restore your gut to health, start by identifying and eliminating the foods that you may be sensitive to. These could be driving autoimmunity, dysbiosis, and inflammatory processes. Gluten is a very common food sensitivity that can lead to immune system dysregulation in the intestines [14, 15, 16, 17].

I suggest that you start with the least level of restrictions and only cut out more potentially troublesome foods if you don’t get good results:

As a first step, remove all highly processed foods that may increase inflammatory processes in the gut and body. 

  • A diet based on simple whole foods and that isn’t heavily grain or dairy based, such as one based on Paleo principles is an excellent way to do this.

If you don’t get symptom improvement after a couple of weeks on Paleo, you may find a plan that eliminates more potentially troublesome foods (e.g. the Autoimmune protocol (AIP) diet to be a better fit for you.

  • AIP hasn’t been tested in gastritis but has shown promise in other autoimmune conditions, including inflammatory bowel disease and Hashimoto’s thyroiditis [32, 33]

Eating slowly and mindfully can also be a great help: In one observational study of people with chronic gastritis, 58% noted that their symptoms of stomach ache and bloating were related to habits such as eating too many sweets and leftovers but also through eating too fast and having irregular meal times [34].


Supporting your diet with the right supplements is very important for helping to improve your autoimmune and digestive conditions.


I would strongly recommend that people with autoimmune gastritis start a regimen of reputable probiotics

There’s not much research looking directly at the benefits of probiotics on autoimmune gastritis specifically. But there are plenty of studies that show probiotics help with autoimmune disease more generally by improving gut health and helping to reduce the gut permeability (leaky gut) that allows allergenic materials to pass into the bloodstream [35, 36].

Probiotics will also help if you have a coexisting H. pylori infection. A 2018 systematic review of 11 studies, including seven randomized controlled studies, found that even alone, multi-strain probiotics eradicated H. pylori in 14% of cases [37].

However, they work best with antibiotics to eradicate the infection. A 2019 systematic review and meta analysis involving nearly 9,000 patients found that, compared with controls, those given probiotics as part of their H. pylori eradication treatment had higher rates of eradication and lower incidences of total side effects [38].

Gut Rebuilding Nutrients (Glutamine and N-Acetyl-Cysteine)

Some amino acid supplements can also help with atrophic and autoimmune gastritis as they help to repair tissues, including the gut lining.

These gut rebuild supplements include glutamine, which in several studies has been shown to help improve the integrity of the gut lining, not specifically for people with autoimmune gastritis, but in those with leaky gut and diarrhea-predominant IBS for example [39].

Also useful is NAC (n-acetylcysteine), which is a very safe and natural amino acid  compound that is also a powerful antioxidant. In one study, NAC helped prevent H. pylori induced gastritis [40] and the supplement has also been shown to enhance gut healing in people with atrophic gastritis [41]. 

Vitamin B12

Because autoimmune gastritis destroys cells that make intrinsic factor, patients with this condition will generally need to take large doses of vitamin B12. 

Research studies on the effect of vitamin B12 in autoimmune gastritis have shown that:

  • Early supplementation with B12 and iron (see below) may prevent anemia and neurological problems [22].
  • Patients testing positive for anti-parietal cell antibodies can see a reduction in positivity following regular intramuscular B12 injections (in this study from100% to 42.9%) [42]. 
  • Two studies have shown that vitamin B12 injections can also help to reduce stomach autoimmunity [43].

Traditionally, vitamin B12 was injected directly into the muscle to get around absorption problems, but this might not always be necessary according to more recent research. Again, it is something I would discuss with patients on a case-by-case basis, but a respected review suggests that high oral doses of vitamin B12 can in some cases be as effective as injections in treating B12 deficiency [44].

Other Supplements

Iron supplements may also be required if you have autoimmune gastritis. Reduced stomach acid makes this mineral hard to absorb, increasing the risk of iron deficiency anemia. 

People with autoimmune gastritis can also be deficient in folic acid, another B vitamin. In this case, it can be worth supplementing this vitamin [25].

To help with poor digestion and low stomach acid symptoms caused by autoimmune gastritis, you may also consider taking a supplement of hydrochloric acid (HCl) and pepsin. It’s always best to monitor your symptoms closely when trialing HCl. If symptoms do not improve within a couple of weeks, it should not be continued (unless otherwise advised by your doctor).

The Bottom Line

Autoimmune gastritis can be tricky to diagnose and can occur alongside a suite of other autoimmune issues, which may complicate diagnosis. 

However tackling the underlying gut health issues and inflammation can be a great help, as can correcting specific deficiencies of Vitamin B12 and stomach acid.

For more guidance, consider scheduling a virtual or in-person consultation at our functional healthcare center.

➕ References

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