Background: Epidemiological research has shown that increased total homocysteine (tHcy) levels are associated with an increased risk of thromboembolic disease; however, controversy still exists over which subtype of stroke is allied to hyperhomocysteinemia. This study aimed to investigate whether elevated tHcy is an independent risk factor for ischemic stroke and to compare tHcy levels in patients with ischemic stroke subtypes.Methods: We performed a case-control study, in which 171 ischemic stroke patients aged over 16 years and 86 age and sex-matched controls were eligible to participate and were enrolled from January 2009 to January 2010. The patients’ demographic data, traditional stroke risk factors, and the results of fasting tHcy, vitamin B12, and folate of serum were collected in the first 5 days after ischemic stroke. Stroke subtypes were classified according to the Trial of Org 10172 in Acute Stroke Treatment (TOAST) criteria. SPSS software (version 13) was used for the statistical analysis of the data, and a P value smaller than 0.05 was considered statistically significant.Results: The mean fasting Hcy levels was significantly higher in the cases (16.2 μmol/L, 95% CI: 14.8 to 17.5) than in the controls (13.5 μmol/L, 95% CI: 12.4 to 14.6) (P=0.013). The mean Hcy levels was elevated significantly in those with cardioembolic strokes compared with the controls (17.7 μmol/L, 95% CI: 14.8 to 20.5; P=0.010). The plasma Hcy level was associated with an adjusted odds ratio of 2.17 (95% CI: 1.24 to 3.79; P=0.004) for Hcy above 15 μmol/L concentration for all types of stroke.Conclusion: Our data showed that elevated serum Hcy is an independent risk factor for ischemic stroke and it has a strong association with cardioembolic subtype.