Understanding the Mechanisms: What Causes Poor B12 Absorption?

October 5, 2025 •

5 min read

A staggering number of people, particularly those over 60, suffer from vitamin B12 deficiency, with some estimates suggesting up to 20% are affected. The most common cause is not a lack of dietary intake, but rather, an underlying issue with absorption. Understanding what causes poor B12 absorption is the first step toward effective management and better health.

Quick Summary

Poor B12 absorption is often linked to digestive issues, autoimmune conditions like pernicious anemia, certain medications, and dietary choices. Age and surgeries can also disrupt the complex process required for B12 uptake.

Key Points

Pernicious Anemia: An autoimmune condition is a primary cause of poor B12 absorption due to the destruction of intrinsic factor-producing stomach cells.
Reduced Stomach Acid: Common in older adults, low stomach acid hinders the initial separation of B12 from food proteins.
Medication Side Effects: Long-term use of metformin and acid-suppressing drugs like PPIs can impair B12 absorption.
Digestive Disorders: Conditions such as Crohn's disease, celiac disease, and SIBO damage the small intestine, disrupting the final absorption step.
Gastric Surgery: Procedures that alter stomach anatomy, including bariatric surgery, dramatically reduce the body's capacity to absorb B12.
Vegan Diets: While not a malabsorption issue, a lack of dietary B12 from animal products is a common cause of deficiency that relies on supplements or fortified foods.

The Complex Process of B12 Absorption

To understand why absorption fails, it is essential to first know how it works. The absorption of vitamin B12 is a complex, multi-step process that begins in the stomach and ends in the small intestine.

Release from food: When you eat animal products containing vitamin B12, hydrochloric acid and the enzyme pepsin in your stomach work together to separate the vitamin from its protein carrier.
Binding to R-protein: The freed B12 molecule then binds with a protein called haptocorrin, also known as R-protein, which protects it from the acidic stomach environment.
Release from R-protein: As the food moves into the small intestine, pancreatic enzymes break down the R-protein, releasing the B12 molecule.
Binding to Intrinsic Factor: B12 must then combine with intrinsic factor (IF), a protein produced by the parietal cells in the stomach.
Absorption in the Ileum: The B12-intrinsic factor complex travels to the terminal ileum, the final section of the small intestine, where it binds to specialized receptors and is absorbed into the bloodstream.

Any disruption at any stage of this intricate pathway can lead to poor B12 absorption.

Gastric and Stomach-Related Causes

The stomach plays a critical role in the initial stages of B12 absorption. Conditions affecting the stomach are therefore a primary cause of malabsorption.

Pernicious Anemia

Pernicious anemia is an autoimmune disorder that leads to vitamin B12 deficiency. The immune system mistakenly attacks the parietal cells of the stomach, which produce both hydrochloric acid and intrinsic factor. Without intrinsic factor, the body cannot absorb B12 from food or supplements, leading to a deficiency. People with this condition often require lifelong vitamin B12 injections.

Atrophic Gastritis

This condition involves the chronic inflammation and thinning of the stomach lining. It is a common cause of B12 deficiency, especially in older adults, because it reduces the production of hydrochloric acid and intrinsic factor. Decreased stomach acid, known as hypochlorhydria, impairs the initial step of freeing B12 from food proteins.

Gastric Surgery

Surgical procedures that remove parts of the stomach, such as gastric bypass or gastrectomy, significantly reduce or eliminate the stomach's ability to produce intrinsic factor and acid. As a result, patients who undergo these procedures are at a very high risk for lifelong B12 malabsorption and require regular supplementation or injections.

Intestinal Factors Inhibiting B12 Uptake

The small intestine is where the final absorption of the B12-intrinsic factor complex occurs. Any disease or condition affecting this part of the digestive tract can impair uptake.

Small Intestinal Bacterial Overgrowth (SIBO)

In SIBO, an excessive amount of bacteria colonizes the small intestine. These bacteria can consume the vitamin B12 before it has a chance to be absorbed by the body. This leads to a deficiency, even if intake is adequate. It is often a result of other gastrointestinal conditions or surgeries.

Inflammatory Bowel Disease (IBD)

Diseases such as Crohn's disease can cause inflammation and damage to the terminal ileum, the precise location where the B12-intrinsic factor complex is absorbed. The chronic inflammation disrupts the delicate absorptive lining, preventing the necessary uptake of the vitamin.

Celiac Disease

An immune reaction to gluten in celiac disease causes damage to the lining of the small intestine. This damage can reduce the surface area available for nutrient absorption, including vitamin B12, along with other critical vitamins and minerals.

Fish Tapeworm Infection

While rare in many parts of the world, infection with the fish tapeworm (Diphyllobothrium latum) can lead to B12 deficiency. The parasite lives in the small intestine and competes with its host for the available vitamin B12.

Medications and Lifestyle Factors Affecting B12 Absorption

Besides physiological conditions, external factors like certain medications and lifestyle choices can also interfere with absorption.

Metformin: This common diabetes medication has been shown to lower vitamin B12 levels over the long term by interfering with its absorption. Regular monitoring is recommended for those on this medication.
Acid-Suppression Drugs: Medications like proton pump inhibitors (PPIs) and H2 blockers, used for acid reflux and ulcers, reduce stomach acid production. This directly impairs the body's ability to free B12 from food proteins, making absorption difficult over time.
Chronic Alcohol Use: Excessive and long-term alcohol consumption can damage the stomach lining and digestive tract, which impairs the absorption of many nutrients, including vitamin B12.
Nitrous Oxide Exposure: Repeated exposure to nitrous oxide, or laughing gas, can interfere with vitamin B12 metabolism. It can inactivate the vitamin, making it unusable by the body.

Comparing Common Causes of Poor B12 Absorption


Feature	Pernicious Anemia	Gastric Surgery	Celiac Disease
Cause	Autoimmune destruction of stomach parietal cells and intrinsic factor.	Surgical removal or bypass of parts of the stomach or small intestine.	Immune reaction to gluten that damages the small intestinal lining.
Mechanism	Complete lack of intrinsic factor, preventing B12-IF complex formation.	Reduced or absent production of intrinsic factor and acid due to surgical changes.	Reduced absorption surface area and damaged intestinal receptors.
Treatment	Lifelong B12 injections or high-dose oral supplements.	Regular B12 supplementation or injections, often for life.	Adherence to a strict gluten-free diet and B12 supplements if needed.
Primary Location	Stomach	Stomach/Intestine	Intestine
Key Symptom	Megaloblastic anemia.	Post-surgical nutritional deficiencies.	Wide range of digestive and systemic issues.

Dietary Considerations and Inadequate Intake

While this article focuses on malabsorption, it is important to acknowledge that dietary inadequacy is also a cause of deficiency, especially among certain populations. Because vitamin B12 is found almost exclusively in animal products, individuals following a strict vegan or vegetarian diet are at a high risk of deficiency if they do not consume fortified foods or supplements. A balanced diet that includes a variety of animal foods can prevent this cause of deficiency.

Conclusion

Vitamin B12 deficiency is a significant health concern that can lead to a variety of neurological and hematological issues, but the reason for the deficiency is often rooted in absorption problems rather than a simple lack of dietary intake. A complex interplay of stomach acid, intrinsic factor, and a healthy intestinal lining is required for the body to properly utilize this essential nutrient. From autoimmune diseases like pernicious anemia to common medications and surgical history, many factors can disrupt this process. For anyone experiencing symptoms of B12 deficiency, it is critical to consult a healthcare professional to identify the root cause. A proper diagnosis is necessary to determine the most effective treatment, which may range from dietary changes and supplements to B12 injections, ensuring that the body receives the B12 it needs to function correctly. For more information on vitamin B12, consult resources from the National Institutes of Health.(https://ods.od.nih.gov/factsheets/VitaminB12-Consumer/)

Frequently Asked Questions

The most common cause of poor B12 absorption is inadequate absorption related to an underlying medical condition, not simply low dietary intake. This is often due to issues with stomach acid, intrinsic factor, or the small intestine's ability to absorb the vitamin.

Pernicious anemia is an autoimmune disease where the body's immune system attacks and destroys the stomach cells that produce intrinsic factor (IF). Since IF is essential for B12 absorption in the small intestine, its absence leads to a severe B12 deficiency.

Yes, long-term use of medications that suppress stomach acid, such as proton pump inhibitors (PPIs) and H2 blockers, can interfere with B12 absorption from food. Stomach acid is needed to release B12 from the proteins in food.

As people age, particularly those over 60, they are more prone to developing decreased stomach acidity, a condition known as hypochlorhydria. This reduced acid production hinders the release of B12 from food, causing poor absorption.

Yes, gastric bypass and other surgeries that alter the stomach and small intestine, are a major cause of poor B12 absorption. These procedures reduce or bypass the part of the gut responsible for producing intrinsic factor and absorbing B12, requiring lifelong supplementation.

While it is an intake issue rather than malabsorption, a strict vegan or vegetarian diet is a significant cause of B12 deficiency because the vitamin is found naturally only in animal products. People on these diets must rely on fortified foods or supplements to meet their B12 needs.

Yes, vitamin B12 deficiency can cause nerve damage and other neurological symptoms even before anemia develops. Symptoms like tingling in the hands and feet, or difficulty with balance, can precede any signs of blood-related issues.

Small Intestinal Bacterial Overgrowth (SIBO) causes poor B12 absorption because the excess bacteria in the small intestine compete with the host for nutrients. The bacteria consume the B12 from food, leaving less for the body to absorb.