Congenital hypoplastic anemias are a rare and heterogeneous group of disorders. This paper reviews new molecular diagnostic tests in two distinct forms of congenital anemias, anemia due to transplacental infection with B19 parvovirus and Fanconi anemia. In both instances, molecular assays making use of amplification of DNA by the polymerase chain reaction have been used to diagnose either a specific viral infection or gene mutation responsible for a disorder. Recognition of these entities has important prognostic and therapeutic implications.