What is the main cause of vitamin B12 deficiency? A comprehensive overview

October 24, 2025 •

4 min read

According to the MSD Manual, the most common cause of vitamin B12 deficiency is inadequate absorption, not simply a low dietary intake. This critical fact highlights that the main cause of vitamin B12 deficiency is often an underlying medical condition, with the most prevalent being the autoimmune disorder pernicious anemia.

Quick Summary

The most significant cause of B12 deficiency is malabsorption, most commonly due to pernicious anemia, though diet, age, and medications also play a role.

Key Points

Malabsorption is the main cause: The most common reason for low B12 is the body's inability to absorb the nutrient properly, not insufficient intake.
Pernicious anemia is a top culprit: This autoimmune disease attacks stomach cells that produce intrinsic factor, which is essential for B12 absorption.
Diet matters, but less often: Inadequate dietary intake is a significant risk for vegans and vegetarians, but it is a less common cause for the general population.
Other health conditions contribute: Gastric surgeries, celiac disease, and Crohn's disease can all interfere with B12 absorption.
Medications can be a factor: Certain drugs, like metformin and PPIs, can reduce B12 levels over time.
Diagnosis is key for proper treatment: Depending on the cause, treatment may require injections or high-dose oral supplements to bypass the absorption issue.

Understanding the Main Driver: Malabsorption

While many people associate vitamin B12 deficiency with a vegan or vegetarian diet, the reality is that poor absorption of the vitamin is the single most common culprit. Your body can't produce vitamin B12, so it must be obtained from food and absorbed through a complex process involving the stomach and intestines. When this process is disrupted, a deficiency can occur, even if you eat plenty of B12-rich foods.

The Role of Intrinsic Factor and Pernicious Anemia

The most frequent cause of malabsorption, and therefore the main cause of vitamin B12 deficiency in many developed countries, is pernicious anemia. This is an autoimmune disease where the body’s immune system mistakenly attacks the parietal cells in the stomach. These cells are responsible for producing intrinsic factor, a special protein that binds to vitamin B12 and enables its absorption in the small intestine.

When these parietal cells are destroyed, intrinsic factor production ceases, and the body can no longer absorb vitamin B12 from food. It is important to distinguish between pernicious anemia and other causes of vitamin B12 deficiency, as the treatment may differ. Since pernicious anemia prevents absorption, dietary changes alone are insufficient, and treatment often requires lifelong B12 injections.

Other Factors Impairing Vitamin B12 Absorption

Beyond pernicious anemia, several other conditions and circumstances can impair the absorption of vitamin B12, leading to a deficiency:

Gastritis: This inflammation of the stomach lining can reduce the production of stomach acid (hydrochloric acid), which is needed to separate vitamin B12 from the protein in food. This is a common cause of deficiency, particularly in older adults.
Gastrointestinal Surgery: Procedures that remove parts of the stomach (gastrectomy) or intestines (gastric bypass, ileal resection) can remove the areas where intrinsic factor is made or where B12 is absorbed, respectively.
Inflammatory Bowel Diseases (IBD): Conditions like Crohn's disease and celiac disease can cause inflammation and damage to the small intestine, disrupting the absorption of nutrients, including B12.
Medications: Certain drugs, including long-term use of proton pump inhibitors (PPIs) for heartburn and metformin for diabetes, can interfere with vitamin B12 absorption.
Intestinal Infections: Infections or bacterial overgrowth in the small intestine, such as a fish tapeworm or blind loop syndrome, can cause organisms to compete with the host for the vitamin.
Alcohol Use Disorder: Chronic and excessive alcohol consumption can damage the digestive system and lead to poor vitamin B12 absorption.

Dietary Insufficiency and Other Causes

While less common as a primary cause in the general population due to the body's ability to store B12 for several years, inadequate dietary intake is a significant risk for specific groups. Vegans and strict vegetarians are at risk because B12 is found almost exclusively in animal products. Without fortified foods or supplements, their intake will be insufficient over time. Infants breastfed by vegan mothers are also at risk.

Comparing B12 Deficiency Causes: Absorption vs. Intake

This table summarizes the key distinctions between the main causes of vitamin B12 deficiency.


Feature	Absorption-Based Deficiency	Intake-Based Deficiency
Primary Mechanism	Body cannot effectively absorb B12 from food due to underlying issues.	Insufficient consumption of B12-rich foods.
Most Common Example	Pernicious anemia (autoimmune destruction of intrinsic factor).	Vegan or long-term vegetarian diet.
Treatment Focus	Addressing the absorption problem, often with injections or high-dose oral supplements bypassing the need for intrinsic factor.	Correcting dietary habits with supplements or fortified foods.
Need for Lifelong Treatment?	Often requires lifelong injections or high-dose supplements if the underlying condition is permanent (e.g., pernicious anemia).	May be reversible with consistent dietary changes or supplementation once levels stabilize.
Time to Develop Symptoms	Can take years for liver stores to deplete, making onset slow and subtle.	Also takes time, but can occur more quickly in infants with low stores.

Diagnosing and Treating Vitamin B12 Deficiency

Diagnosis of vitamin B12 deficiency is typically made through blood tests, which may include a complete blood count (CBC) to check for megaloblastic anemia and a direct vitamin B12 test. Further tests, such as methylmalonic acid (MMA) and homocysteine levels, may be used for a more definitive diagnosis, as these can be elevated in a B12 deficiency. In cases of suspected pernicious anemia, tests for intrinsic factor antibodies may be performed.

Treatment depends on the root cause and severity. For those with pernicious anemia or other severe absorption issues, injections of hydroxocobalamin are the standard treatment, initially given frequently and then moving to a maintenance schedule. For dietary-related deficiencies or mild malabsorption, high-dose oral supplements can be effective. It is crucial to identify the correct cause to ensure appropriate and effective treatment.

Conclusion

In summary, while dietary factors like a vegan diet are a known cause, the most common and significant cause of vitamin B12 deficiency is malabsorption. This is most often caused by the autoimmune condition pernicious anemia, which prevents the body from absorbing the vitamin from food. Other conditions, including gastrointestinal surgeries, diseases like Crohn's, and certain medications, also play a significant role. Correctly identifying the main cause is the first step toward effective management, as treating an absorption problem is different from simply increasing dietary intake. Anyone experiencing symptoms of B12 deficiency should consult a healthcare provider for proper diagnosis and a personalized treatment plan.

It is always advisable to discuss any health concerns with a medical professional and to get regular check-ups, especially if you fall into one of the higher-risk categories for malabsorption.

Frequently Asked Questions

Pernicious anemia is an autoimmune disease where the body's immune system attacks the stomach cells that produce intrinsic factor. Intrinsic factor is required to bind with vitamin B12 for it to be absorbed in the intestines, so its absence leads to a severe absorption problem and a deficiency.

Yes, since vitamin B12 is found primarily in animal products, individuals following a vegan diet are at high risk of deficiency if they do not regularly consume fortified foods or take supplements.

Surgeries like gastric bypass or a gastrectomy can remove parts of the stomach responsible for producing intrinsic factor, or parts of the small intestine where absorption occurs, leading to a permanent malabsorption problem.

No, not all do. While severe malabsorption, like that caused by pernicious anemia, often requires injections, some milder absorption issues or dietary deficiencies can be effectively treated with high-dose oral supplements.

Symptoms can include fatigue, weakness, numbness or tingling in the hands and feet, a sore tongue, cognitive issues like confusion or memory loss, and in severe cases, more serious neurological damage.

Older adults are more susceptible because they are more prone to developing decreased stomach acid (gastritis), which is necessary to release B12 from food proteins before it can be absorbed.

Medications that can interfere with B12 absorption include metformin, which is used for diabetes, and proton pump inhibitors (PPIs) used to reduce stomach acid for conditions like heartburn.

For those with absorption problems like pernicious anemia, standard oral supplements are often not effective, necessitating injections to bypass the digestive tract. For dietary-related deficiencies, oral supplements are typically sufficient.