The inner lining of blood vessels, known as the endothelium, is sensitive to irritation or abrasion. High levels of homocysteine have been shown to cause endothelial damage and thus initiate the atherosclerotic lesions that lead to heart disease, stroke, Alzheimer's disease, and senile dementia.

Elevated Homocysteine levels are associated with a wide variety of other diseases including:

• depression
• multiple sclerosis
• diabetes
• birth defects
• Alzheimer's disease
• rheumatoid arthritis
• osteoporosis

Homocysteine is located at a junction of several key metabolic pathways in the body. It is an intermediate in the synthesis of cysteine from methionine. A deficiency of vitamin B-12, folic acid, and/or vitamin B-6 can block this pathway, causing buildup of toxic levels of homocysteine. Supplementation of these nutrients facilitates the pathway, reducing homocysteine levels.