Understanding the Medical Conditions: What medical conditions can cause low B12?

October 8, 2025 •

3 min read

According to the National Institutes of Health, vitamin B12 deficiency is common in older adults and can also be caused by various underlying health issues. While diet is a factor, many people are left wondering what medical conditions can cause low B12, even with an adequate intake of the vitamin.

Quick Summary

Several medical conditions, including autoimmune disorders, specific gastrointestinal diseases, and certain medications, can lead to impaired vitamin B12 absorption. Surgeries affecting the stomach or small intestine also prevent adequate B12 intake, necessitating careful management and monitoring.

Key Points

Pernicious Anemia: An autoimmune condition where the body cannot produce or use intrinsic factor, a protein essential for B12 absorption.
Gastrointestinal Disorders: Chronic inflammatory conditions like Crohn's disease and celiac disease can damage the parts of the intestine responsible for B12 absorption.
Medication Side Effects: Long-term use of certain drugs, including metformin for diabetes and proton pump inhibitors for acid reflux, can lead to reduced B12 levels.
Surgical Consequences: Gastric and bariatric surgeries can reduce or eliminate intrinsic factor production and bypass the intestine's absorption site, necessitating lifelong B12 supplementation.
Hidden Factors: Other conditions such as chronic pancreatitis, small intestinal bacterial overgrowth (SIBO), and even parasitic infections can impair B12 absorption.
Diagnosis is Key: Symptoms can be subtle, so proper diagnosis through blood tests is crucial, especially for those with risk factors like autoimmune disease or certain medication use.

The Complex Process of Vitamin B12 Absorption

To understand why medical conditions can lead to low B12 levels, it's essential to first grasp the complex process of its absorption. The vitamin, ingested from animal products or fortified foods, must be liberated from its protein carriers by stomach acid. It then binds to a protein called intrinsic factor, secreted by the stomach's parietal cells. This complex travels to the terminal ileum in the small intestine for absorption. Any interference in this pathway can cause deficiency.

Autoimmune Conditions as a Root Cause

Autoimmune diseases are a significant cause of impaired B12 absorption.

Pernicious Anemia

This common autoimmune cause of B12 deficiency involves the immune system attacking stomach parietal cells or intrinsic factor, preventing B12 absorption. It develops slowly, and those with other autoimmune disorders face a higher risk.

Atrophic Gastritis

Often associated with pernicious anemia, this condition thins the stomach lining, damaging parietal cells and reducing acid and intrinsic factor production crucial for B12 absorption. Helicobacter pylori infection is also a cause.

Gastrointestinal Disorders Impairing Absorption

Digestive tract issues can directly hinder B12 absorption:

Crohn's Disease: Inflammation, especially in the terminal ileum, where B12 is absorbed, can cause malabsorption.
Celiac Disease: Damage to the small intestine from gluten can lead to B12 deficiency if the terminal ileum is affected.
Small Intestinal Bacterial Overgrowth (SIBO): Excess bacteria in the small intestine can consume B12.
Chronic Pancreatitis: Insufficient pancreatic enzymes can impair B12 release from binding proteins.
Fish Tapeworm Infection: The parasite competes for B12, leading to deficiency.

Medications and Surgeries Affecting B12 Levels

Certain medications and procedures can compromise B12 absorption.

Medications

Long-term use of some drugs can interfere with B12 absorption, particularly those reducing stomach acid:

Metformin: This diabetes drug can reduce B12 absorption.
Proton Pump Inhibitors (PPIs) and H2 Receptor Antagonists: Acid-reducing medications can impair B12 absorption with long-term use.

Surgical Procedures

Surgeries altering the digestive tract often require lifelong B12 supplementation:

Bariatric Surgery: Procedures like gastric bypass affect stomach size and bypass absorption sites.
Gastrectomy: Removal of the stomach eliminates intrinsic factor production.
Ileal Resection: Removal of the terminal ileum eliminates the main B12 absorption site.

Other Causes of Low B12

Additional factors can lead to B12 deficiency:

Chronic Alcoholism: Damages stomach lining and liver, reducing acid/intrinsic factor and impairing storage.
HIV/AIDS: Can cause malabsorption.
Genetic Disorders: Rare hereditary conditions can impair B12 absorption from birth.

Comparison of Medical Conditions Causing Low B12

The table below outlines common medical conditions that can lead to low B12 levels, detailing their primary mechanism, impact on intrinsic factor, common treatment, and the typical onset of the deficiency. For a comprehensive list, consult a medical professional.


Medical Condition	Primary Mechanism	Impact on Intrinsic Factor	Common Treatment	Onset of Deficiency
Pernicious Anemia	Autoimmune destruction of parietal cells, leading to a lack of intrinsic factor.	Impairs or destroys intrinsic factor.	Lifelong B12 injections or high-dose oral supplements.	Slow, can take years to develop.
Atrophic Gastritis	Inflammation and thinning of the stomach lining, reducing acid and intrinsic factor production.	Reduces production of intrinsic factor.	Address the underlying cause (e.g., H. pylori), plus B12 supplementation.	Gradual.
Crohn's Disease	Inflammation damages the terminal ileum, the site of B12 absorption.	Indirect impact; intrinsic factor production is normal but absorption is hindered.	Manage inflammation, supplement with B12, often via injection.	Varies based on disease severity and location.
Gastric Bypass Surgery	Alters the digestive tract, bypassing the part of the stomach and small intestine where B12 is absorbed.	Reduces or eliminates intrinsic factor production.	Lifelong B12 supplementation, often high-dose oral or injections.	Post-surgical, ongoing.
Long-term Metformin Use	Can interfere with the absorption of B12 in the intestine.	No impact.	Monitor B12 levels; supplement if low.	Gradual, with long-term use.

Conclusion

Beyond dietary factors, numerous medical conditions can disrupt B12 absorption. Autoimmune diseases like pernicious anemia, gastrointestinal disorders such as Crohn's and celiac, and medications like metformin and acid-suppressing drugs are common culprits. Surgeries altering the digestive tract also pose a lifelong risk. If a B12 deficiency is suspected or risk factors are present, consult a healthcare provider for diagnosis and management. Untreated deficiency can lead to severe, irreversible neurological damage. For more information, refer to the {Link: National Institutes of Health Office of Dietary Supplements https://ods.od.nih.gov/factsheets/VitaminB12-HealthProfessional/}.

Disclaimer: This article is for informational purposes only and does not constitute medical advice. Consult with a qualified healthcare provider for any health concerns or before making any decisions related to your health or treatment.

Frequently Asked Questions

Intrinsic factor is a special protein produced by the stomach's parietal cells that binds to vitamin B12, allowing it to be absorbed in the small intestine. Without it, B12 cannot be properly assimilated into the body.

Yes, long-term use of gastric acid inhibitors like proton pump inhibitors (PPIs) and H2 blockers can interfere with the release of stomach acid, which is needed to free B12 from food for absorption.

Bariatric surgeries, such as gastric bypass, reduce the size of the stomach and often bypass the part of the small intestine that produces intrinsic factor and absorbs B12. This significantly impairs absorption.

Pernicious anemia is a specific type of vitamin B12 deficiency caused by an autoimmune condition that prevents the body from absorbing B12 due to a lack of intrinsic factor. Other medical issues or poor diet can also cause B12 deficiency.

Not all people with Crohn's disease develop low B12. The risk is higher when the disease causes inflammation in or requires surgical removal of the terminal ileum, where B12 is absorbed.

Yes, chronic alcohol abuse can damage the stomach and liver. It can reduce the production of stomach acid and intrinsic factor, and also interfere with the liver's ability to store B12, leading to a deficiency.

Treatment depends on the cause. For absorption issues like pernicious anemia or post-bariatric surgery, lifelong vitamin B12 injections or high-dose oral supplements are often required. Addressing the underlying condition is also important.