This chapter, reviews mitochondrial and other selective metabolic causes of stroke. In MELAS, despite the microangiopathic findings in the brain and muscles, the stroke-like episodes are more likely attributed to mitochondrial and metabolic dysfunction in neural tissue and glia rather than to ischemic vascular pathology. Kearns Sayre syndrome (KSS) is a mitochondrial disorder caused by large heteroplasmic deletions in mtDNA. Brain infarction, presumably secondary to cardioembolic sources, may occur. Hyperhomocysteinemia is a clinical syndrome caused by several enzyme deficiencies in methionine metabolism. Patients with homocystinuria have markedly elevated plasma homocysteine concentrations. Most patients present with peripheral venous thrombosis, including pulmonary embolism. Stroke, peripheral arterial occlusions, or myocardial infarction can be the initial presentation. The increased tendency for thrombosis usually presents as an ischemic stroke. Metabolic stroke due to hypoxemia and vascular insufficiency may occur in methylmalonic acidemia. Metabolic causes of stroke are quite heterogeneous.