Thrombocytopenia is a relatively common clinical problem in hospitalized neonates, and it is critical to distinguish infants who have rare congenital thrombocytopenias from those who have acquired disorders. Two well-described inherited thrombocytopenia syndromes that present in the newborn period are congenital amegakaryocytic thrombocytopenia (CAMT) and thrombocytopenia with absent radii (TAR). Although both are characterized by severe (< 50,000/microL) thrombocytopenia at birth, the molecular mechanisms underlying these disorders and their clinical presentations and courses are distinct. CAMT is an autosomal recessive disorder caused by mutations in the thrombopoietin (TPO) receptor c-Mpl. TAR is a syndrome of variable inheritance and unclear genetic etiology consisting of thrombocytopenia in association with bilateral absent radii and frequently additional congenital abnormalities. This article summarizes the current understanding of the pathophysiology and clinical course of CAMT and TAR.