We present a case of a late-preterm infant admitted for suspected cyanotic heart disease who was found to have a thrombosed ductus arteriosus. Maternal history was significant for heterozygosity for Factor V Leiden, treated with enoxaparin during her pregnancy, and congenital hearing loss. The neonate did not have a Factor V Leiden mutation detected, but was found to have a heterozygous mutation within the MFTHR gene. He was treated with anticoagulation, with improving hemodynamics measured by echocardiogram. This case presents a rare disease, which is potentially fatal if diagnosis is delayed.