Objective To investigate the relationship between cerebral microbleeds (CMBs) and different subtypes of ischemic stroke and its prognosis.Methods Totally 116 patients with ischemic stroke in our hospital from March 2014 to May 2016 were enrolled in this study. According to the Chinese ischemic stroke subclassification system, there were 5 subtypes of ischemic stroke, including large artery atherosclerosis (LAA), cardiogenic stroke (CS), stroke with other etiology (OE), penetrating artery disease (PAD), and stroke with undetermined etiology (UE). Then the patients in each subtype were divided into CMBs group and non-CMBs group. The related serum markers were compared between groups. Logistic regression analysis was used to determine the influencing factors for CMBs in each subtype of ischemic stroke, and the National Institutes of Health Stoke Scale was used to evaluate the prognosis of each subtype with CMBs.Results Serum homocysteine (Hcy) level in the PAD group was 23.32±2.79 μmol/L, significantly higher than 20.64±3.11 μmol/L in the LAA group, 20.7±2.63 μmol/L in the CS group, 18.92±2.91 μmol/L in the OE group, and 17.63±3.06 μmol/L in the UE group (P<0.05). Serum hemoglobin A1 (HbA1) level was 7.60±0.25 in the OE group and 7.11±0.32 in the LAA group, which were both significantly higher than 5.03±0.11 in the CS group, 5.10±0.11 in the PAD group, and 4.99±0.12 in the UE group (P<0.05), but there was no significant difference in HbA1 level between the OE and LAA groups or between the CS, PAD, and UE groups (P>0.05). Long-term alcohol consumption was an independent risk factor for CMBs in CS and PAD. Hcy was an independent risk factor for CMBs in each subtype of ischemic stroke. HbA1 was an independent risk factor for CMBs in PAD and LAA.Conclusions Hcy, HbA1, and long-term alcohol consumption are independent risk factors for CMBs in ischemic stroke. The prognosis of ischemic stroke with CMBs is not significantly different between different subtypes.