The Methylation Support Protocol
A test-first protocol for raised homocysteine and methylation status. Layer 0 is measurement — fasting homocysteine, serum B12 with methylmalonic acid if borderline, folate, kidney and thyroid function, and a medication review — because the commonest causes of a high result are B12 deficiency, kidney decline, metformin or acid suppression. Layer 1 is B12, Layer 2 is folate (methylfolate or folic acid, both work), Layer 3 is riboflavin for known MTHFR 677TT carriers, Layer 4 is optional TMG. B6 is deliberately excluded. Includes the honest scope: lowering homocysteine has not prevented heart attacks in trials; it may reduce stroke where flour is not fortified.
Daily Schedule
Timing and dosage for each step
Layer 1 — once daily, from week 0 (everyone who proceeds past testing)
500 mcg
500 mcg cyanocobalamin or methylcobalamin — the form does not matter. If serum B12 was low or MMA raised, use 1–2 mg daily: in a Cochrane review, 1 mg oral matched injections and 2 mg exceeded them. B12 goes first because folate given into an undiagnosed B12 deficiency can correct the anaemia while nerve damage continues. ⚠ Neurological symptoms (numbness, unsteady gait, memory change) need a clinician, not a supplement.
Layer 2 — with breakfast, from week 0 if folate is low, otherwise from week 4 if homocysteine is still raised
400 mcg
400 mcg L-5-MTHF, or 400 mcg folic acid — both lowered homocysteine equally in a 24-week trial, and folic acid worked in MTHFR TT carriers. 0.4 mg gives about 90% of the maximum homocysteine reduction; 0.8 mg gives all of it; more adds nothing. ⚠ Keep total folate from all supplements at or below 1 mg/day (EU upper limit). Planning pregnancy: folic acid 0.4–0.8 mg is the form with outcome evidence.
Layer 3 — with food, from week 4 (known MTHFR 677TT carriers only)
1.6 mg
1.6 mg — the trial dose, roughly the daily requirement. In TT carriers it lowered homocysteine 22% and systolic blood pressure 5.6–13 mmHg; no effect in CC or CT. Small trials from one research group, unreplicated — hence grade C. If you have not been genotyped, do not test just for this layer; skip it.
Layer 4 — optional, split morning and evening, from week 8 (homocysteine still above ~15 µmol/L after Layers 1–3)
4000 mg
4 g betaine daily, split into two doses to limit the fishy body odour seen above 3 g. Meta-analysis of five trials at ≥4 g/day: homocysteine −1.2 µmol/L. A small backup pathway, not a first-line lever. If homocysteine is still above 15 µmol/L at this point, look harder for a cause (kidney function, thyroid, medication) before adding anything.
Read This Before the Protocol
This protocol treats a number, and the number is mostly a messenger. Raised homocysteine is a sensitive signal for vitamin B12 deficiency, reduced kidney function, overt hypothyroidism, metformin or long-term acid suppression, smoking and heavy unfiltered coffee. Finding which of those applies is worth more than lowering the result.
The second thing to know: lowering homocysteine has not prevented heart attacks. A Cochrane review of 15 randomised trials in 71,422 people found no effect on myocardial infarction (RR 1.02) or death (RR 1.01). Stroke fell by 10%, with the benefit concentrated where flour is not fortified with folic acid. A trial in older adults with mild cognitive impairment found slower brain atrophy when homocysteine was above about 11 µmol/L. Those are the outcomes this protocol can reasonably claim. The evidence is laid out in Homocysteine: What Your Level Means and How to Lower It.
And the third: you do not need an MTHFR test to run it. The genetics guideline advises against routine testing; homocysteine answers the question directly. See MTHFR Variants: What the Evidence Actually Supports.
Layer 0 — Test First
| Test | Why |
|---|---|
| Fasting homocysteine (repeat if high, sample processed promptly) | The target; a single value can be falsely raised by slow processing |
| Serum B12 (+ methylmalonic acid or holotranscobalamin if 150–300 pmol/L) | The commonest treatable cause; MMA separates B12 from folate deficiency |
| Serum or red-cell folate | Low folate is common where flour is not fortified |
| Creatinine / eGFR | Kidney decline raises homocysteine and changes what helps |
| TSH | Overt hypothyroidism raises it; treatment lowers it |
| Medication review | Metformin, PPIs, H2 blockers, methotrexate, anticonvulsants, nitrous oxide exposure |
If homocysteine is in the typical range (below about 12 µmol/L) and B12 and folate are normal, stop here. There is no evidence that pushing a normal level lower does anything.
The Layer Logic
| Layer | What | Evidence grade | Who |
|---|---|---|---|
| 0 — Test | Find the cause | — | Everyone |
| 1 — Vitamin B12 | 0.5 mg (1–2 mg if deficient) | A for correcting deficiency | Everyone who proceeds |
| 2 — Folate | 0.4 mg methylfolate or folic acid | A for lowering homocysteine | Low folate, or still raised at week 4 |
| 3 — Riboflavin | 1.6 mg | C | Known MTHFR 677TT only |
| 4 — TMG | 4 g | C | Optional; still raised at week 8 |
The protocol is graded C — to its weakest layer that some users will rely on. Layers 1 and 2 on their own are grade A for what they do to homocysteine.
Layer 1 — Vitamin B12
B12 goes first for a safety reason as much as an efficacy one: folate can mask the anaemia of B12 deficiency while nerve damage progresses. 500 mcg daily maintains status in most people. If B12 was low or MMA raised, 1–2 mg daily orally corrects it — in a Cochrane review, 1 mg oral matched intramuscular injections and 2 mg exceeded them. Cyanocobalamin and methylcobalamin are equivalent; buy on price. Profile: Vitamin B12.
Layer 2 — Folate
0.4 mg of folate takes homocysteine down by about 20%; 0.8 mg by 23%; doses above that add nothing. Methylfolate and folic acid both work. In head-to-head trials they lowered homocysteine equally, and folic acid lowered it by 20% in MTHFR TT carriers — more than in any other genotype. Methylfolate avoids unmetabolised folic acid in blood, which is a preference, not a proven benefit. Planning a pregnancy: folic acid 0.4–0.8 mg is the recommendation, whatever your genotype. Profile: Methylfolate.
Layer 3 — Riboflavin (TT Carriers Only)
If you already know you are MTHFR 677TT, riboflavin 1.6 mg daily lowered homocysteine by 22% in a 12-week trial and lowered systolic blood pressure by 5.6–13 mmHg in two others — effects not seen in other genotypes. The dose is the daily requirement and carries no risk; the evidence is small and from one group. If you also have high blood pressure, tell whoever manages it. Profile: Riboflavin.
Layer 4 — TMG (Optional)
Betaine re-methylates homocysteine through a backup pathway in the liver and kidney. At 4 g/day or more it lowered homocysteine by about 1.2 µmol/L in a meta-analysis of five small trials. That is a small effect with a fishy-odour side effect above 3 g. Use it only if homocysteine remains raised after Layers 1–3 and no other cause has been found. Profile: TMG.
What Is Deliberately Left Out
- Vitamin B6. It does not lower fasting homocysteine in meta-analyses, and supplemental B6 causes sensory neuropathy; the EU upper limit is now 12 mg/day. Count the B6 in your multivitamin, B-complex and magnesium products and keep the total under that. See Vitamin B6.
- High-dose "methylation" complexes. In one post-heart-attack trial, folic acid plus B12 plus B6 showed a borderline increase in cardiovascular events. Use the doses that work.
- SAMe, NAC, choline megadoses. Not tested for this purpose.
Interactions and Stop Rules
- Metformin — B12 falls about 19% over four years; Layer 1 is especially relevant.
- Methotrexate, phenytoin, carbamazepine, valproate — folate interacts in both directions. Do not start Layer 2 without the prescriber.
- Levodopa — not affected by this protocol (no B6), but check any B-complex you add.
- Stop and see a clinician if you develop numbness, tingling, unsteadiness or memory change; if homocysteine is above 30 µmol/L; or if eGFR is reduced.
Monitoring
| Marker | When | Target |
|---|---|---|
| Fasting homocysteine | Baseline, week 8–12 | Back into the typical range for age; no proven benefit below that |
| B12 (+ MMA) | Baseline, week 12 if deficient | MMA normalised |
| Folate | Baseline | Adequate |
| Blood pressure (TT carriers on Layer 3) | Monthly | Trend, alongside existing treatment |
| eGFR, TSH | Baseline | Rule out non-vitamin causes |
If homocysteine has not fallen at 12 weeks despite adherence, the answer is a better search for the cause — not a fifth supplement.