The prediction of functional outcome in patients with acute cerebral infarction depends on many factors. Various techniques have been applied to predict severity and outcome after cerebral infarction. Neuron-specific enolase (NSE) is a component of a specific brain enzyme and a useful marker of brain injury. We evaluated the relation between initial serum NSE level and short- and long-term clinical outcome in 59 patients with acute cerebral infarction and in 38 age-matched healthy controls. Serum NSE levels were determined in patients with carotid artery (CA) territory cerebral infarction within 24 hours of onset. Brain MRI was performed four to seven days after stroke. Patients were divided into two groups: large CA territory infarction with a lesion extending cortex (cortex group), and small subcortical CA territory infarction (subcortical group) with a lesion confined to the subcortical white matter. We compared the initial serum NSE levels of the two groups. National Institute of Health Stroke Scale (NIHSS) was determined at admission and seven days after onset and the modified Rankin's scale was used at the 3 months follow-up after onset. Serum NSE levels were significantly elevated in patients with acute cerebral infarction compared with the normal controls (13.88 ± 5.47 ng/dl vs. 8.15 ± 1.53 ng/dl, p < 0.05). The initial ( < 24 h) serum NSE level was higher in the cortical group than in the subcortical group (16.68 ± 5.70 ng/dl vs. 10.98 ± 3.34 ng/dl, p < 0.05). NIHSS on admission and on the 7th day correlated with the initial serum NSE level (p < 0.05), as were more severe functional outcomes, as determined 3 months after onset (p < 0.05). This study shows that initial serum NSE level may be a useful marker for severity in acute ischemic stroke, and that it may be well correlated with short-term and long-term functional outcomes.