Most autoimmune diseases are rare in infants. Early onset can represent an extreme phenotype arising from strong genetic predisposition relatively independent of environmental influence. Alternatively, neonatal autoimmunity can arise from transplacental passage of maternal pathogenic IgG autoantibodies. Distinguishing between these possible explanations is crucial for determining the prognosis in the specific patient, and has important implications for understanding pathogenesis. We report a case of neonatal thrombotic stroke associated with both cardiolipin and β2-glycoprotein I antibodies in neonatal serum but absent from cord blood and maternal serum. While the child also carried one prothrombotic allele of factor V (Leiden allele), which may have contributed to the risk of thromboembolic disease, the serological analysis represents unequivocal evidence of de novo neonatal primary phospholipid antibody syndrome.