Antiphospholipid antibodies are a recognised prothrombotic risk factor associated with acute ischaemic infarction. Most autoimmune diseases are rare in infants, and in the neonatal period, autoimmunity is related to transplacental passage of maternal immunoglobulin G autoantibodies. Distinguishing between de novo and acquired autoimmunity has important therapeutic implications and is crucial for determining the prognosis. We present a case of a neonatal thrombotic stroke associated with de novo synthesis of antiphospholipid antibodies, a homozygous 1298C/C methylene-tetrahydrofolate reductase mutation and a double-homozygous plasminogen activator inhibitor 1 polymorphism (PAI-1 844A/A and 675 4G/4G), which may have increased the final thrombotic risk. Her mother was not positive for antiphospholipid antibodies. The authors highlight an unequivocal evidence of a de novo case of paediatric antiphospholipid antibody syndrome and emphasise the need for a thorough investigation in cases of neonatal stroke including molecular thrombophilia study.