Low vitamin B12 most often comes down to one of two problems: you’re not getting enough from your diet, or your body can’t absorb what you’re eating. The second category is far more common than most people realize, and it includes everything from autoimmune conditions to common medications. Most labs flag B12 levels below 200 to 250 pg/mL as deficient, while levels between 200 and 300 pg/mL are considered borderline low.
How Your Body Absorbs B12
Understanding why B12 drops requires a quick look at how it gets into your bloodstream, because the process is surprisingly fragile. When you eat B12-containing food, your stomach acid first separates the vitamin from the protein it’s bound to. Then a protein called intrinsic factor, made by specialized cells in your stomach lining, attaches to the freed B12. This intrinsic factor-B12 pair travels to the end of your small intestine, where it’s finally absorbed into your blood.
Any disruption along this chain, from stomach acid production to intrinsic factor to the intestinal lining itself, can leave you deficient even if your diet is packed with B12-rich foods. That’s why some people eat plenty of meat and dairy and still end up with low levels.
Pernicious Anemia and Autoimmune Causes
The most well-known cause of B12 malabsorption is pernicious anemia, an autoimmune condition where your immune system attacks the cells lining your stomach. These are the same cells that produce intrinsic factor. Without enough intrinsic factor, your body simply can’t carry B12 from your gut into your bloodstream. Your immune system may also produce antibodies that directly block intrinsic factor from doing its job, creating a double barrier to absorption.
Pernicious anemia is especially common in older adults and in people of Northern European descent, though it can develop at any age. It’s typically diagnosed through blood tests that check for the specific antibodies targeting your stomach lining and intrinsic factor. Because the absorption pathway is completely blocked, people with pernicious anemia usually need B12 delivered by injection or high-dose oral supplements rather than relying on food sources.
Stomach Changes With Age
As you get older, the lining of your stomach gradually thins in a condition called atrophic gastritis. This destroys parietal cells, the same cells responsible for making both stomach acid and intrinsic factor. With less stomach acid, your body struggles to release B12 from food. With less intrinsic factor, it can’t absorb the B12 that does get released. Adults over 60 are particularly prone to developing B12 deficiency through this mechanism, and it tends to show up as a specific type of anemia where red blood cells become abnormally large.
Chronic infection with H. pylori bacteria can accelerate this process at any age, damaging the stomach lining years before age-related thinning would normally become a problem.
Medications That Interfere With B12
Two of the most widely prescribed drug classes can quietly drain your B12 over time. Metformin, taken by millions of people with type 2 diabetes, is now recognized as causing B12 deficiency in up to 1 in 10 people who take it. The longer you’re on it, the higher the risk. Proton pump inhibitors (PPIs), used for acid reflux, work by suppressing stomach acid production. Since stomach acid is the first step in freeing B12 from food, years of PPI use can gradually deplete your stores.
If you’ve been on either of these medications for more than a year or two, periodic B12 monitoring is a reasonable precaution. Deficiency from medications tends to develop slowly, so symptoms may creep up over months or years without an obvious cause.
Diet: Vegans and Vegetarians at Highest Risk
B12 is found almost exclusively in animal products: meat, fish, eggs, and dairy. People who avoid all animal foods are at striking risk. Studies estimate that roughly 52% of vegans have deficient B12 levels, compared to just 1% of people eating a typical mixed diet. One European study found deficiency rates as high as 92% in vegans and 77% in vegetarians who ate eggs and dairy but didn’t supplement.
The rates drop significantly among vegans who take B12 supplements or regularly consume fortified foods like nutritional yeast, plant milks, or fortified cereals. Without those sources, though, plant-based diets provide virtually zero B12. Your liver stores enough B12 to last several years, which means deficiency symptoms may not appear until long after you’ve changed your diet. This delay can make it hard to connect the dots.
Intestinal Diseases and Surgical Causes
Because B12 is absorbed at the very end of the small intestine (the terminal ileum), any disease affecting that stretch of gut can cause deficiency. Crohn’s disease frequently targets the terminal ileum, making B12 malabsorption one of its common nutritional complications. Celiac disease, which damages the intestinal lining, more often affects iron and folate absorption since it primarily hits the upper small intestine. However, in advanced celiac disease that extends further down the gut, B12 absorption can be impaired as well.
Weight loss surgeries pose a significant risk. Gastric bypass reroutes food past much of the stomach and upper intestine, reducing both acid production and the surface area available for absorption. Studies show B12 deficiency prevalence of about 13% in bariatric surgery patients, with rates climbing in the years following the procedure. Lifelong B12 supplementation is standard care after gastric bypass for this reason.
Genetic Factors
Certain genetic variations affect how your body processes B12 once it’s absorbed. Mutations in the MTHFR gene, which controls a key step in converting one amino acid (homocysteine) into another (methionine), can negatively impact B12 levels in the blood. This mutation primarily disrupts the methylation pathway, essentially the biochemical cycle where B12 does its work. The result is that even with adequate B12 intake, your body may not use it efficiently, and blood levels can drop.
MTHFR mutations are relatively common, affecting an estimated 10 to 15% of the population to varying degrees. Most people with these variants never develop clinical deficiency, but the mutation can tip the balance when combined with other risk factors like a less-than-ideal diet or mild absorption issues.
How Low B12 Is Identified
A standard blood test measures your serum B12 level. Most labs consider anything below 200 to 250 pg/mL deficient, but the gray zone matters. Levels between 200 and 300 pg/mL are considered borderline, and many people in this range already have symptoms. When results fall in that borderline territory, a follow-up test measuring methylmalonic acid (MMA) in the blood can clarify things. MMA rises when your body doesn’t have enough usable B12, making it a more sensitive marker than serum B12 alone.
If you fall into any of the higher-risk groups, from taking metformin to eating a plant-based diet to being over 60, testing is straightforward and inexpensive. B12 deficiency is one of the more reversible nutritional problems when caught early, but nerve damage from prolonged deficiency can become permanent, which makes identifying the cause and correcting it worth prioritizing.