Although relatively rare, thromboembolic events are a major complication of invasive procedures, mainly vascular catheterization, required for the survival of neonates admitted to the neonatal intensive care unit. Sometimes symptoms may be ambiguous and the diagnosis may not be immediate. The clinical relevance of polymorphism of methilene tetrahydrofolate reductase (MTHFR) gene heterozigosity and of omocystein level in the genesis of these thromboembolic events are poorly understood. We report two cases of thrombosis of the abdominal aorta, mimicking aortic coarctation, in two neonates, successfully treated at diagnosis with 170 UI/Kg of low molecular weight heparin (LMWH) twice daily, without side effects. Screening for prothrombotic defects revealed the heterozygosity for MTHFR C677T in both neonates and low omocystein level in one of them. We suggest that in newborns vascular thrombosis should be considered in the differential diagnosis of acute disorders of blood circulation at birth and familial thrombophilia should be investigated. LMWH therapy with a dose of 170 UI/Kg twice daily usually allows vascular recanalization, without side effects.