L-lysine is an amino acids with a pharmacological use much more specific than that of most other amino acids. So far, supplementation of l-lysine is one of the best options available for the treatment of herpes simplex virus infections, especially oral forms. L-lysine is also much cheaper than antiviral drugs such as Acyclovir. L-lysine supplementation works by tilting the balance between lysine and arginine heavily in favor of lysine. This ameliorates herpes outbreaks because the herpes virus depends on the presence of arginine for its replication.

Lysine in combination with arginine is used by bodybuilders for the combination's alleged effect of stimulating the release of growth hormone.

Lysine has also been shown to be useful in the prevention of atherosclerosis, a hardening of the walls of arteries caused by deposits of lipoproteins (fats). Lysine may be capable of loosening and preventing such deposits, therefore keeping artery walls flexible. Thus, there is less susceptibility for hypertension (high blood pressure). Hypertension is a major factor in heart attack and stroke.