Two infants with congenital microcephaly associated with the factor V Leiden mutation are described. In both cases, brain magnetic resonance imaging (MRI) revealed cerebral atrophy and porencephalic cystic lesions, which were probably attributable to prenatal cerebral vascular events. These findings suggest that assessment for this mutation is an important part of the evaluation of infants with unexplained congenital microcephaly, especially in cases with infarcts and/or porencephalic cysts on brain MRI.