Homocysteine is an amino acid that is normally present in very small amounts in the blood.  Normally the vitamins B6, B12, and folate quickly convert homocysteine to other products but when there is a deficiency of these vitamins leaves the amino acid in the blood at higher than normal levels.  There is some evidence that excess homocysteine is linked to atherosclerosis allowing blood clots to form and causing damage to blood vessel walls.

Excess homocysteine is also found in people with a rare genetic disorder called homocystinuria caused by a dysfunctional enzyme that is required for metabolism.  The buildup of this enzyme and homocysteine in infants can cause serious health issues including failure to thrive and people with the disease may develop heart or blood vessel diseases at an early age.