What Disease Depletes B12? A Comprehensive Guide

October 19, 2025 •

4 min read

According to the National Institutes of Health, pernicious anemia is the most common cause of vitamin B12 deficiency in many developed countries. However, this isn't the only condition that can lead to depleted B12 levels, as a range of digestive and autoimmune diseases can interfere with your body's ability to absorb this vital nutrient.

Quick Summary

Several diseases interfere with the body's ability to absorb vitamin B12, causing deficiency. The most common is pernicious anemia, an autoimmune disorder. Other culprits include atrophic gastritis, Crohn's disease, and celiac disease, all affecting nutrient absorption in the gastrointestinal tract.

Key Points

Pernicious Anemia: The most common disease depleting B12, caused by an autoimmune attack on stomach cells that produce intrinsic factor, a protein essential for B12 absorption.
Atrophic Gastritis: This chronic stomach inflammation reduces both the stomach acid and intrinsic factor needed to absorb B12 from food.
Crohn's Disease: Inflammation from this IBD often affects the ileum, the specific part of the small intestine where B12 is absorbed, leading to deficiency.
Celiac Disease: Damage to the small intestine lining from gluten exposure in untreated celiac disease can cause malabsorption of B12 and other nutrients.
Post-Surgery Malabsorption: Gastric surgeries, including gastric bypass, can reduce the area for B12 absorption, necessitating lifelong supplementation.
Neurological and Anemic Symptoms: Chronic B12 depletion can cause serious issues, including megaloblastic anemia and neurological damage like fatigue, tingling, and memory problems.
Diagnosis and Treatment: Proper diagnosis requires professional testing to identify the cause; treatment often involves B12 injections or high-dose oral supplements to correct the deficiency.

The Importance of Vitamin B12 and How It Is Absorbed

Vitamin B12, also known as cobalamin, is a crucial nutrient for the body's proper functioning. It is essential for producing healthy red blood cells, ensuring the nervous system works correctly, and synthesizing DNA. A deficiency can lead to a wide array of symptoms, from fatigue and weakness to more severe neurological problems.

The absorption process of vitamin B12 is complex. First, stomach acid helps detach the vitamin from the food it's bound to. It then combines with a protein called intrinsic factor, produced by parietal cells in the stomach lining. This B12-intrinsic factor complex travels to the small intestine, specifically the ileum, where it is finally absorbed into the bloodstream. Any disease that disrupts this multi-step process can lead to a deficiency, even if your dietary intake is sufficient.

Pernicious Anemia: The Primary Culprit

Pernicious anemia is an autoimmune disorder and the most frequently cited cause of severe vitamin B12 deficiency, particularly in older adults. In this condition, the body's immune system mistakenly attacks its own healthy cells in the stomach, specifically the parietal cells responsible for producing intrinsic factor. Without enough intrinsic factor, the body cannot absorb vitamin B12 effectively from food, regardless of how much is consumed. This leads to a gradual but significant depletion of the body's B12 stores, which can result in megaloblastic anemia and neurological damage if left untreated.

Other Diseases that Cause B12 Depletion

Beyond pernicious anemia, several other medical conditions can lead to B12 deficiency by interfering with absorption. These diseases primarily affect the stomach and small intestine, disrupting the delicate processes required for vitamin uptake.

Gastrointestinal Diseases

Atrophic Gastritis: This condition involves the chronic inflammation and thinning of the stomach lining. This damage reduces the stomach's production of both hydrochloric acid and intrinsic factor, severely hindering B12 absorption. It is often a precursor to pernicious anemia.
Crohn's Disease: As an inflammatory bowel disease (IBD), Crohn's can cause chronic inflammation throughout the digestive tract. Since it frequently affects the ileum—the site of B12 absorption—the disease can impair the body's ability to take in the vitamin, leading to deficiency.
Celiac Disease: This autoimmune disorder triggers an inflammatory response in the small intestine when gluten is consumed, damaging the intestinal lining. While a gluten-free diet often normalizes B12 levels, untreated celiac disease can cause malabsorption of B12 and other nutrients.
Small Intestinal Bacterial Overgrowth (SIBO): An excess of bacteria in the small intestine can consume the vitamin B12 before it can be absorbed by the body. This effectively 'steals' the nutrient, leaving the host deficient.
Gastric Surgery: Procedures like gastric bypass surgery for weight loss, or the surgical removal of parts of the stomach or small intestine, can significantly reduce the areas where intrinsic factor is produced and B12 is absorbed. Patients undergoing these procedures typically require lifelong B12 supplementation.

Other Autoimmune and Endocrine Disorders

Autoimmune Thyroid Disease and Type 1 Diabetes: Pernicious anemia and other autoimmune conditions often cluster together. Individuals with autoimmune thyroid disease or type 1 diabetes have a higher risk of developing pernicious anemia, which in turn causes B12 deficiency.
Graves' Disease: As another autoimmune disorder, Graves' disease has been linked to a higher risk of developing pernicious anemia and subsequent B12 deficiency.

A Comparison of Major Diseases Causing B12 Depletion


Feature	Pernicious Anemia	Atrophic Gastritis	Crohn's Disease	Celiac Disease
Cause	Autoimmune destruction of parietal cells, leading to intrinsic factor deficiency.	Chronic inflammation and thinning of the stomach lining, reducing intrinsic factor and acid.	Chronic inflammation of the digestive tract, often affecting the ileum where B12 is absorbed.	Autoimmune reaction to gluten, damaging the small intestine lining.
Mechanism	Loss of intrinsic factor prevents B12 absorption in the ileum.	Reduced intrinsic factor and stomach acid impair B12 release from food and binding.	Inflammation and damage to the ileum directly prevent B12 absorption.	Damage to the intestinal villi impairs nutrient absorption in the small intestine.
Treatment	Lifelong B12 injections or high-dose oral supplements, bypassing the need for intrinsic factor.	Vitamin B12 injections or high-dose oral supplements; addressing the underlying inflammation if possible.	Managing the underlying inflammatory disease and providing B12 supplementation.	A strict gluten-free diet, which often corrects the deficiency over time; supplementation may be needed initially.
Key Symptom	Megaloblastic anemia, neurological issues, sore tongue.	Can be asymptomatic or have symptoms of B12 deficiency.	Abdominal pain, fatigue, diarrhea, weight loss, sometimes B12 deficiency symptoms.	Diarrhea, weight loss, fatigue, sometimes B12 deficiency symptoms.

Conclusion

While a variety of factors can contribute to low vitamin B12 levels, from diet to certain medications, it is often an underlying medical condition, particularly a disease that impairs absorption, that is the root cause. Pernicious anemia stands out as a common autoimmune disease directly targeting the absorption mechanism. However, other gastrointestinal issues like atrophic gastritis, Crohn's disease, and celiac disease can also severely impact your B12 status. Diagnosing the specific disease is crucial for effective treatment, which often involves B12 supplementation to replenish the body's stores and prevent long-term neurological damage.

For those with chronic conditions or post-surgical changes to their digestive system, consistent monitoring and lifelong treatment are often necessary to maintain healthy B12 levels. If you experience persistent fatigue, tingling, or other symptoms associated with B12 deficiency, it is vital to consult a healthcare professional to identify and address the root cause.

Authoritative Reference

National Heart, Lung, and Blood Institute: Vitamin B12–Deficiency Anemia

Note: Consult with a healthcare professional for a proper diagnosis and treatment plan if you suspect a vitamin B12 deficiency.

Frequently Asked Questions

The most common disease is pernicious anemia, an autoimmune condition where the body's immune system attacks and destroys the stomach cells that produce intrinsic factor, a protein necessary for absorbing vitamin B12.

Yes, Crohn's disease is a major cause of B12 deficiency. It is an inflammatory bowel disease that often affects the ileum, the last part of the small intestine where B12 is absorbed, impairing the body's ability to take it in.

Yes, atrophic gastritis, or thinning of the stomach lining, is a disease that can lead to B12 deficiency. It reduces the production of intrinsic factor and stomach acid, both of which are needed for B12 absorption.

Yes, if a medical condition like pernicious anemia or gastric surgery prevents you from absorbing B12 from food, you will likely need lifelong supplementation. This is often done via injections or high-dose oral supplements.

Yes, untreated celiac disease can cause B12 deficiency due to the inflammation and damage it causes to the small intestine, impairing nutrient absorption. Adhering to a gluten-free diet is key to reversing this.

If left untreated, chronic vitamin B12 deficiency can lead to severe and potentially irreversible nerve damage, memory loss, depression, and megaloblastic anemia.

Yes, gastric bypass surgery is a significant risk factor for B12 deficiency because it alters the digestive tract, reducing the areas where intrinsic factor and B12 are produced and absorbed.