Congenital extremity anomalies have many modes of presentation. Interruption of vascular supply with thrombophily is a rare cause of congenital extremity absence. Here it is presented a 7 mth old male with absence of the left lower extremity. Laboratory tests revealed Factor V Leiden and Prothrombin G20210A heterozygote mutation and that was as the cause of extremity absence. At the patients with congenital extremity absences, it is not imprudent to explore a possible thrombophilic mutation along with other known etiologic factors.