Neonatal thrombosis is a serious event that can cause mortality or severe morbidity. Newborn-related factors, including genetic prothrombotic risk factors, may affect the occurrence of neonatal thrombosis. In this report, a case of intrauterine iliofemoral arterial thrombosis associated with mild hyperhomocysteinemia caused by methylenetetrahydrofolate reductase 677C-T gene mutation is presented. We suggest that methylenetetrahydrofolate reductase gene mutation might be investigated in neonates and their families presenting with thromboembolic disease.