What illnesses cause vitamin B12 deficiency?

November 13, 2025 •

3 min read

According to the National Institutes of Health, between 3% and 43% of older adults experience vitamin B12 deficiency, often due to underlying health conditions rather than a lack of dietary intake. A variety of illnesses can interfere with the body's ability to absorb or utilize this essential nutrient, leading to deficiency and a cascade of potential health problems.

Quick Summary

Several medical conditions, including autoimmune disorders such as pernicious anemia, and gastrointestinal diseases like celiac and Crohn's, can disrupt the body's absorption of vitamin B12. Surgical procedures and long-term use of certain medications also contribute significantly to the risk of developing a deficiency.

Key Points

Autoimmune Attack: Pernicious anemia is a common cause of B12 deficiency, where the immune system destroys stomach cells needed for absorption.
Gastric Issues: Conditions like atrophic gastritis and H. pylori infection reduce stomach acid and intrinsic factor, hindering B12's release and absorption.
Intestinal Damage: Celiac disease and Crohn's disease damage the small intestine, impairing its ability to absorb vitamin B12.
Surgical Impact: Gastric bypass and other stomach or intestinal surgeries are a major risk factor due to altered anatomy affecting B12 absorption.
Bacterial Interference: Small Intestinal Bacterial Overgrowth (SIBO) can cause deficiency by allowing bacteria to consume the vitamin before the body can absorb it.
Neurological Consequences: Untreated B12 deficiency can lead to severe and potentially irreversible neurological problems like nerve damage, memory loss, and cognitive decline.
Accurate Diagnosis: Proper diagnosis requires identifying the specific underlying illness, as treatment strategies vary significantly based on the cause.

Autoimmune and Gastric-Related Illnesses

One of the most common reasons the body fails to absorb vitamin B12 is related to stomach conditions, especially autoimmune diseases.

Pernicious Anemia

Pernicious anemia is an autoimmune condition where the body's immune system attacks the parietal cells in the stomach lining. These cells are responsible for producing a protein called intrinsic factor, which is essential for vitamin B12 absorption. Without intrinsic factor, the body cannot absorb vitamin B12 from the diet, regardless of how much is consumed. This condition is more prevalent in older adults and those of Northern European descent.

Atrophic Gastritis

Atrophic gastritis is characterized by chronic inflammation and thinning of the stomach lining. This damage can reduce or eliminate the production of both hydrochloric acid and intrinsic factor, both of which are critical for processing and absorbing vitamin B12. Autoimmune atrophic gastritis is caused by the body's immune system attacking its own stomach cells, while environmental atrophic gastritis is often caused by a chronic Helicobacter pylori bacterial infection.

Intestinal and Malabsorption Disorders

Beyond the stomach, diseases affecting the small intestine can directly impair the final stage of vitamin B12 absorption.

Crohn's Disease

This inflammatory bowel disease (IBD) causes chronic inflammation throughout the digestive tract, particularly affecting the small intestine. If the inflammation is located in the ileum—the final section of the small intestine where the intrinsic factor-B12 complex is absorbed—it can lead to severe vitamin B12 deficiency. Crohn's disease can also necessitate the surgical removal of part of the ileum, further exacerbating malabsorption.

Celiac Disease

An immune reaction to gluten that causes damage to the small intestine's lining, celiac disease can also disrupt vitamin B12 absorption. When left untreated, the damage to the intestinal villi reduces the surface area available for nutrient uptake. A strict, gluten-free diet is the standard treatment and can allow the intestine to heal and absorption to improve.

Small Intestinal Bacterial Overgrowth (SIBO)

An overgrowth of bacteria in the small intestine can interfere with nutrient absorption. Some bacteria can consume vitamin B12 before the body has a chance to absorb it, leading to a deficiency even if intrinsic factor production is normal.

Surgical Procedures

Several types of gastrointestinal surgeries, including gastric bypass and procedures that remove part or all of the stomach (gastrectomy) or the ileum, can dramatically affect vitamin B12 absorption. These surgeries reduce the capacity to produce intrinsic factor or bypass the key absorption site, requiring lifelong monitoring and supplementation.

Comparison of Illnesses Causing B12 Deficiency


Illness	Mechanism of Deficiency	Primary Affected Area	Treatment Approach
Pernicious Anemia	Autoimmune destruction of intrinsic factor-producing cells.	Stomach	B12 injections for life
Atrophic Gastritis	Inflammation and thinning of stomach lining, reducing acid and intrinsic factor production.	Stomach	Treat underlying cause (e.g., H. pylori), B12 supplements/injections
Crohn's Disease	Inflammation in the ileum, impairing absorption.	Small Intestine	Address inflammation, may need injections
Celiac Disease	Small intestine damage due to gluten reaction, impairing absorption.	Small Intestine	Strict gluten-free diet, supplements
Bariatric Surgery	Removal or bypass of stomach/small intestine section.	Stomach & Small Intestine	Lifelong B12 supplementation, often injections
SIBO	Bacteria consume B12 before it can be absorbed.	Small Intestine	Antibiotics, dietary changes, B12 supplements

Conclusion

Identifying the root cause is crucial for effective treatment of vitamin B12 deficiency. While inadequate dietary intake is a factor for vegans and vegetarians, a significant number of cases are caused by underlying medical conditions that interfere with absorption. Whether it's an autoimmune attack in pernicious anemia, inflammatory damage from Crohn's or celiac disease, or the after-effects of gastrointestinal surgery, addressing the specific illness is key to resolving the deficiency. Early diagnosis and appropriate medical management, which may include injections or high-dose oral supplements, can prevent long-term neurological complications associated with prolonged vitamin B12 deficiency. For individuals with a diagnosed illness that impacts B12 absorption, consistent medical follow-up is essential.

For more information on the clinical diagnosis and management of B12 deficiency, see the resources provided by the National Institutes of Health.

Frequently Asked Questions

Pernicious anemia is often cited as the most common cause of clinically evident vitamin B12 deficiency globally. It is an autoimmune condition that prevents the absorption of B12 by attacking the intrinsic factor protein necessary for absorption.

Yes, celiac disease can cause vitamin B12 deficiency because the damage to the small intestine's lining impairs the absorption of nutrients. The inflammatory response to gluten damages the intestinal villi, reducing the effective surface area for nutrient uptake, including B12.

Crohn's disease causes inflammation throughout the digestive tract. If the inflammation occurs in the final section of the small intestine (ileum), where vitamin B12 is absorbed, it can directly prevent the body from taking in the nutrient.

Surgical procedures on the stomach or small intestine, such as gastric bypass or a gastrectomy, can cause a vitamin B12 deficiency. This is because these surgeries reduce the number of cells that produce intrinsic factor or bypass the section of the intestine where absorption occurs, necessitating long-term supplementation.

Yes, bacterial infections like H. pylori can lead to atrophic gastritis, which reduces stomach acid and intrinsic factor production. Similarly, Small Intestinal Bacterial Overgrowth (SIBO) causes bacteria to consume the available B12, leading to malabsorption.

Yes, older adults are at a higher risk because they are more prone to conditions like atrophic gastritis, which reduces stomach acid needed to release vitamin B12 from food. The ability to absorb B12 from food often diminishes with age.

Certain medications, including long-term use of heartburn drugs (like proton pump inhibitors and H2 blockers) and metformin for diabetes, can reduce vitamin B12 levels over time. These drugs interfere with stomach acid production, which is necessary for B12 absorption.