NIH ODS summarizes the causes as "difficulty absorbing vitamin B12 from food, lack of intrinsic factor (e.g., because of pernicious anemia), surgery in the gastrointestinal tract, prolonged use of certain medications... and dietary deficiency." Those collapse into two mechanisms.
Cause 1: Malabsorption
This is the larger category, and it means the B12 is present in the diet but not getting in.
- Pernicious anemia. NIH ODS describes it as an irreversible autoimmune disease attacking the stomach's parietal cells, eliminating intrinsic factor. Present in about 15–25% of older adults with B12 deficiency.
- Atrophic gastritis. Affects 2% of the general population but 8–9% of adults 65 and older, reducing both intrinsic factor and stomach acid.
- Gastrointestinal surgery and conditions such as celiac disease.
- Medications. NIH ODS names metformin and proton pump inhibitors as drugs that may affect B12 levels.
- H. pylori infection, which NIH ODS links to malabsorption in older adults.
Cause 2: Low dietary intake
NIH ODS notes that "natural food sources of vitamin B12 are limited to animal foods," so vegans and vegetarians carry higher risk, as do infants of women following vegan diets.
This cause is more predictable — it follows directly from a known dietary pattern — which is why it is often easier to identify.
Why the distinction is clinically important
NIH ODS makes a relevant point: people who cannot absorb B12 from food often absorb free B12 normally, so their deficiency "tends to be less severe" than in those lacking intrinsic factor. The mechanism affects what actually corrects the problem, which is a decision for a clinician rather than a shelf.
It also matters because malabsorption causes are often themselves conditions worth diagnosing. B12 deficiency can be the first visible sign of something upstream.
Working out which applies to you
Diet is self-evident. Absorption usually is not, which is why identifying the mechanism requires a doctor. Our free assessment covers both the dietary and medication-related risk factors.
References
This article summarizes published guidance from the sources linked above. It is general information, not medical advice, and it cannot tell you whether you personally have a deficiency. Only a clinician ordering the right test can do that. If you have symptoms that concern you, speak to a doctor.