Vitamin B deficiency typically comes from one of three sources: not getting enough B vitamins in your diet, a medical condition that blocks absorption, or a medication that depletes your stores over time. Because the B vitamins are a group of eight different nutrients, the specific cause depends partly on which B vitamin is low. But a few patterns show up repeatedly.
Diet and Lifestyle
The most straightforward cause is simply not eating enough foods that contain B vitamins. Each B vitamin has its own food sources, so restrictive diets can create gaps in different ways. Vitamin B12 is found almost exclusively in animal products like meat, fish, eggs, and dairy. People who follow a vegan diet without supplementing or eating fortified foods are at significant risk for B12 deficiency. Folate (B9) comes from vegetables like broccoli, asparagus, and Brussels sprouts, as well as chickpeas, peas, and brown rice. A diet that’s generally unbalanced or heavily processed can leave you short on folate.
Heavy alcohol use is one of the most common lifestyle-related causes, and it hits multiple B vitamins at once. Alcohol is particularly damaging to thiamine (B1) levels. It reduces the gut’s ability to absorb thiamine by up to 50%, cuts intestinal absorption overall by as much as 70%, and impairs the body’s ability to use whatever thiamine it does take in. On top of that, people who drink heavily often eat poorly, compounding the problem. Severe thiamine deficiency from chronic alcohol use can lead to a dangerous brain condition called Wernicke’s encephalopathy, which causes acute confusion, memory problems, difficulty with balance, and abnormal eye movements. Alcohol also interferes with folate absorption and is a recognized risk factor for folate deficiency.
Autoimmune Conditions
Pernicious anemia is the most common cause of vitamin B12 deficiency in the UK and a major cause worldwide. It’s an autoimmune condition where your immune system attacks the cells in your stomach that produce a protein called intrinsic factor. This protein is essential for absorbing B12. Without it, the B12 in your food passes through your digestive system without ever reaching your bloodstream. Pernicious anemia develops gradually and can go unnoticed for years before symptoms like fatigue, numbness, or cognitive changes appear.
Digestive Conditions That Block Absorption
Even if your diet includes plenty of B vitamins, your body may not be absorbing them properly. Several digestive conditions interfere with this process.
Crohn’s disease is a key example. B12 is absorbed in the last section of the small intestine, called the ileum. Crohn’s disease commonly causes inflammation in exactly that area. If you’ve had surgery to remove part or all of the ileum, absorbing enough B12 from food alone becomes very difficult.
Celiac disease, an autoimmune reaction to gluten, damages the lining of the small intestine and can reduce absorption of folate and other B vitamins. Any condition that causes chronic inflammation in the gut, including inflammatory bowel disease more broadly, can make it harder for your body to pull nutrients from food. Certain IBD medications, including sulfasalazine and methotrexate, also interfere specifically with folic acid absorption, creating a double hit.
Stomach surgeries, including procedures that remove part of the stomach (gastrectomy), increase the risk of B12 deficiency. The stomach produces both acid and intrinsic factor, both of which are needed to extract and absorb B12 from food. Removing part of the stomach reduces both.
Aging and Stomach Acid Decline
As you get older, the lining of your stomach gradually thins in a process called chronic atrophic gastritis. This leads to a loss of the specialized cells that produce stomach acid and intrinsic factor. Without enough acid, your body can’t separate B12 from the proteins in food. Without enough intrinsic factor, even freed B12 can’t be absorbed. People over 60 are more likely to develop B12 deficiency through this mechanism, and it often shows up as a type of anemia where red blood cells are abnormally large.
This age-related decline is slow and often silent. Many older adults don’t realize they’re becoming deficient until symptoms like fatigue, poor balance, or memory problems develop.
Medications That Deplete B Vitamins
Several widely prescribed medications can lower your B vitamin levels over time. The two most significant are metformin and proton pump inhibitors (PPIs).
Metformin, used by millions of people to manage type 2 diabetes, is now recognized as a common cause of B12 depletion. It may affect up to 1 in 10 people who take it, with higher doses and longer treatment duration increasing the risk. UK drug regulators have updated prescribing guidance to recommend periodic B12 monitoring for people on metformin, particularly those who develop signs of anemia or nerve-related symptoms like tingling or numbness.
PPIs, commonly used for acid reflux and ulcers, reduce stomach acid production. Since stomach acid is needed to release B12 from food, long-term PPI use can gradually drain B12 stores. Nitrous oxide, sometimes used in dental procedures or recreational settings, also inactivates B12 in the body and can trigger acute deficiency in people whose levels are already borderline.
Pregnancy and Increased Demand
Sometimes deficiency happens not because intake dropped, but because the body’s needs increased. Pregnancy is the clearest example. Folate requirements rise sharply during pregnancy because the vitamin is critical for early fetal development. Neural tube defects, which are serious birth defects of the brain and spine, develop in the first few weeks of pregnancy, often before a person even knows they’re pregnant.
The CDC recommends that all women capable of becoming pregnant get 400 micrograms of folic acid daily. Those who have had a previous pregnancy affected by a neural tube defect are advised to take 4,000 micrograms daily, starting at least one month before conception and continuing through the first three months of pregnancy. Because timing matters so much, supplementing before pregnancy is more protective than starting after a positive test.
Genetics and Folate Processing
Variations in a gene called MTHFR have received a lot of attention as a possible cause of folate deficiency. The MTHFR gene helps your body convert folate into its active form. More than half of the U.S. population carries one or two copies of the C677T variant of this gene.
The actual impact, however, is modest. People with two copies of the variant (the TT genotype) have blood folate levels only about 16% lower than those without the variant, when folic acid intake is the same. The CDC’s position is clear: your folic acid intake matters more than your MTHFR genotype in determining your folate levels. In other words, the genetic variant slightly reduces efficiency, but adequate dietary intake largely compensates for it.
How Deficiency Is Confirmed
If you suspect a B vitamin deficiency, a blood test is the starting point. For B12, a serum level below 200 pg/mL is generally considered low, and a level below 150 pg/mL is diagnostic for deficiency. These tests catch most cases, with sensitivity around 95 to 97%.
The tricky part is when your B12 level falls in the low-normal range but you have symptoms. In that situation, a follow-up test measuring methylmalonic acid provides a more direct look at whether your body is actually using B12 properly. Elevated methylmalonic acid suggests a functional deficiency even when serum B12 looks acceptable. This test is particularly useful for older adults and others at high risk who may have borderline blood levels.