Background: We evaluated whether serum antibody levels against individual periodontal pathogens are significantly associated with ischemic stroke subtypes and their risk factors. Methods: Patients with acute ischemic stroke (n=132; 74 male and 58 female, 71.3±10.7 years) and patients with no previous stroke (n=77; 38 male and 39 female, 70.7±9.5 years) were consecutively enrolled in this study. Stroke subtype was evaluated based on the TOAST classification. Serum was obtained from each patient after obtaining the patient’s consent to participate in this study. The levels of serum antibodies against Aggregatibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Prevotella intermedia (Pi) were evaluated by ELISA. Results: The serum-antibody level of Pi was significantly higher in atherothrombotic-stroke patients than in patients with no previous stroke (p<0.005). Serum anti-Pg antibody was significantly associated with atrial fibrillation (overall X2=35.5, R2=0.18, n=209, p<0.001; anti-Pg antibody: odds ratio 4.36 [95%CI 1.71-12.10], p<0.005), and serum anti-Pi antibody was significantly associated with bulb/internal carotid artery atherosclerosis after controlling for the statistically selected associated factors (overall X2=46.1, R2=0.18, n=209, p<0.001; anti-Pg antibody: odds ratio 16.58 [95%CI 3.96-78.93], p<0.001). The levels of serum anti-Pi antibody were significantly associated with atherothrombotic stroke with the statistically selected associated factors excluding bulb/ICA atherosclerosis (overall X2=77.0, R2=0.44, n=129, p<0.001; anti-Pi antibody: odds ratio 23.6 [95%CI 2.65-298.2], p=0.008). However, when we included bulb/ICA atherosclerosis into this model, the levels of serum anti-Pi antibody were no longer significantly associated with atherothrombotic stroke (overall X2=98.0, R2=0.56, n=129, p<0.0001; anti-Pi antibody: p=0.107). Conclusions: Our results suggest that anti-Pg antibody is associated with atrial fibrillation and anti-Pi antibody is associated with carotid artery atherosclerosis. Additionally, anti-Pi antibody may be associated with atherothrombotic stroke through its association with carotid artery atherosclerosis.