What underlying conditions cause low B12?

October 8, 2025 •

3 min read

According to studies, a significant portion of older adults, up to 43% in some communities, have a vitamin B12 deficiency due to malabsorption. Understanding what underlying conditions cause low B12 is crucial for proper diagnosis and treatment, as low intake is not the only factor. For many, the problem is not a lack of B12 in their diet, but rather their body’s inability to process and absorb it effectively.

Quick Summary

Low B12 levels are primarily caused by impaired absorption from conditions like autoimmune gastritis, surgical removal of stomach or intestines, certain medications, and dietary limitations.

Key Points

Autoimmune Attack: Pernicious anemia, a common cause of B12 deficiency, is an autoimmune condition that prevents the production of intrinsic factor, which is essential for B12 absorption.
Gastrointestinal Surgery Impact: Procedures like gastric bypass or removal of parts of the stomach or small intestine can prevent the proper absorption of B12, necessitating long-term supplementation.
Medication Side Effects: Long-term use of certain medications, notably metformin for diabetes and proton pump inhibitors (PPIs) for acid reflux, can lower B12 levels by disrupting absorption or decreasing stomach acid.
Digestive Diseases: Chronic conditions like Crohn's disease and celiac disease cause inflammation and damage to the intestines, which can interfere with the body's ability to absorb vitamin B12 effectively.
Dietary Insufficiency: Strict vegan diets, without supplementation or fortified foods, are a significant risk factor for B12 deficiency because the nutrient is primarily found in animal products.
Age-Related Issues: Older adults are at increased risk for low B12 due to decreased stomach acid production, a condition known as atrophic gastritis, which impairs absorption from food.
Genetic Factors: Rare genetic disorders can cause a selective inability to absorb vitamin B12, requiring medical intervention.

The complex process of B12 absorption

Vitamin B12 absorption requires stomach acid to release B12 from food proteins, then binding with intrinsic factor produced in the stomach, before being absorbed in the small intestine. Disruptions at any stage can lead to deficiency.

Major underlying conditions causing low B12

Low B12 levels can result from various medical conditions and lifestyle factors that interfere with absorption.

Autoimmune disorders

Pernicious Anemia, a common cause, is an autoimmune disease where the body attacks stomach cells, preventing intrinsic factor production necessary for B12 absorption. Autoimmune Atrophic Gastritis similarly causes inflammation and thinning of the stomach lining, reducing acid and intrinsic factor. Other autoimmune diseases are also linked to B12 deficiency.

Gastrointestinal surgeries

Surgery on the stomach or small intestine can significantly impair B12 absorption. Gastrectomy removes the source of intrinsic factor, while bariatric surgery and terminal ileum resection bypass or remove areas crucial for absorption.

Digestive system diseases

Conditions like Crohn's disease and Celiac disease cause inflammation or damage in the small intestine, hindering B12 absorption. Chronic Pancreatitis can affect enzymes needed to release B12 from carrier proteins. Bacterial overgrowth in the small intestine can lead to bacteria consuming B12.

Medications

Certain long-term medications can interfere with B12 absorption. Metformin for type 2 diabetes and Proton Pump Inhibitors (PPIs) and H2 Blockers for acid reflux reduce stomach acid, impacting B12 release from food.

Dietary restrictions

Vegans are at high risk due to B12 being primarily in animal products; supplementation or fortified foods are essential as liver stores deplete over time.

Other conditions and risk factors

Risk factors include aging, which often involves reduced stomach acid, repeated nitrous oxide exposure, chronic alcohol abuse, HIV, and rare genetic disorders like Imerslund-Gräsbeck syndrome.

Comparison of B12 deficiency causes


Cause	Mechanism	Affected Population	Typical Treatment	Key Identifier
Autoimmune (Pernicious Anemia)	Immune system attacks stomach cells, preventing intrinsic factor production	Most common in older adults, often with Northern European ancestry	B12 injections or high-dose oral supplements	Anti-intrinsic factor antibodies; lack of intrinsic factor
Gastrointestinal Surgery	Bypasses or removes parts of the stomach or intestine where B12 is absorbed	Post-bariatric surgery, post-gastrectomy patients	Lifelong B12 injections or high-dose oral supplements	Surgical history (e.g., gastric bypass, gastrectomy)
Digestive Diseases (Crohn's, Celiac)	Chronic inflammation or damage to the small intestine	Individuals diagnosed with Crohn's or Celiac disease	Manage underlying disease; B12 supplements or injections	Active intestinal inflammation or damage
Medications (Metformin, PPIs)	Drug-induced interference with B12 absorption or stomach acid production	Patients on long-term medication for diabetes or acid reflux	Monitor B12 levels, potential supplementation or alternative medication	Medication usage history
Dietary Restrictions (Veganism)	Lack of B12-rich animal products in the diet	Strict vegans or vegetarians not taking supplements	Regular B12 supplements or fortified foods	Dietary history; lack of animal product consumption

Untreated low B12: What happens next?

Untreated B12 deficiency can lead to severe issues, particularly neurological damage. This includes Megaloblastic Anemia, characterized by large red blood cells, nerve damage leading to tingling, numbness, and walking difficulties, cognitive problems like confusion and memory loss, and other symptoms like a sore tongue.

Conclusion

Low B12 stems from various causes, not just diet. Autoimmune conditions, surgeries, digestive diseases, and medications impair absorption. Older adults and vegans are at higher risk. Identifying the cause is vital for treatment, often involving supplementation. Early diagnosis prevents severe neurological issues. Consult a healthcare professional if you suspect low B12. More details are available on the NIH Health Professional Fact Sheet.

Frequently Asked Questions

The most common cause of B12 deficiency, especially in older adults, is pernicious anemia, an autoimmune condition that prevents the stomach from producing intrinsic factor needed for absorption.

Metformin can reduce the absorption of vitamin B12 in the small intestine. Long-term use requires monitoring B12 levels and potentially taking supplements.

Yes, celiac disease can cause low B12. The inflammatory damage to the lining of the small intestine from celiac disease can prevent the proper absorption of many nutrients, including B12.

Vegans are at risk because natural food sources of vitamin B12 are primarily found in animal products. Without fortified foods or supplements, their intake is insufficient to meet the body's needs.

Yes, gastric bypass and other bariatric surgeries can cause B12 deficiency because they alter the digestive tract, bypassing the parts of the stomach and small intestine where B12 absorption occurs.

Reduced stomach acid, often seen with aging or use of medications like PPIs, makes it harder for the body to release vitamin B12 from food proteins, though it does not affect absorption from supplements.

Neurological symptoms can include numbness or tingling in the hands and feet, memory problems, confusion, irritability, difficulty with balance and walking, and, in severe cases, dementia.