Congenital Amegakaryocytic Thrombocytopenia (CAMT) is a rare disorder of infancy characterized by isolated thrombocytopenia along with hypoplasia or aplasia of megakaryocytes in the bone marrow. It is caused by c-mpl mutation which disrupts the function of thrombopoietin (TPO) receptor. CAMT in association with physical anomalies is a rare entity with only limited data from single case reports being available. Here we present a case of 35 days neonate who had CAMT together with facial malformations and cardiac defects.