The cause of perinatal arterial ischemic stroke is unknown in most cases. We explored whether genetic polymorphisms modify the risk of perinatal arterial ischemic stroke. In a population-based case-control study of 1997–2002 births at Kaiser Permanente Northern California, we identified 13 white infants with perinatal arterial ischemic stroke. Controls included 86 randomly selected white infants. We genotyped polymorphisms in 9 genes involved in inflammation, thrombosis or lipid metabolism that have been previously linked with stroke, and compared genotype frequencies in case and control individuals. We tested the following polymorphisms: TNF-α-308, IL-6, lymphotoxin A, factor V Leiden, MTHFR 1298 and 667, prothrombin 20210, and apolipoprotein E ε2 and ε4 alleles. Patients with perinatal arterial ischemic stroke were more likely than controls to have at least one apolipoprotein E ε4 allele (54% vs. 25%, p=0.03). More patients with perinatal arterial ischemic stroke carried two ε4 alleles than did controls (15% vs. 2%, p=0.09), though this finding was not statistically significant. Proinflammatory and prothrombotic polymorphisms were not associated with perinatal arterial ischemic stroke in this small study. The apolipoprotein E polymorphism may confer genetic susceptibility for perinatal arterial ischemic stroke. Larger population-based studies are needed to confirm this finding.