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People with both homocystinuria and factor V Leiden have an increased risk of thrombosis, the formation of blood clots that block blood vessels. Factor V Leiden is a mutated form of factor V that does not respond to activated protein C, an anti-clotting factor. Researchers measured homocysteine levels, partial-thromboplastin times, and analyzed the factor V gene in 45 members of 7 families. Each family had at least one person who had a pair of genes for homocystinuria. Of the 7 people with homocystinuria and factor V Leiden, all but one had thrombosis. The one exception was a baby who had only one factor V Leiden gene and had received anticlotting therapy from birth. Among the 4 people with homocystinuria but no factor V Leiden, none had thrombosis. Three women in one family who had one gene for each homocystinuria and factor V Leiden had spontaneous abortions and circulation disorders in their placentas.

Hyperhomocysteinemia and low concentrations of folate and vitamin B6 appear to be associated with an increased risk of carotid artery stenosis in the elderly. Hyperhomocysteinemia is a condition in which plasma levels of homocysteine are higher than normal. Inadequate folate and vitamin B6 concentrations in the blood are associated with the condition. A group of 1,041 people over the age of 66 were divided into two groups based upon the severity of stenosis in two carotid vessels. People with high levels of homocysteine were found to be twice as likely to be in the group with more severe stenosis than those with normal homocysteine concentrations. Higher concentrations of folate and B6 in the plasma were related to less stenosis, while lower concentrations of folate and B6 were found in patients with more severe sclerosis.