Abstract: The present invention relates to the identification of fetal specific nucleic acids and fetal cell markers in maternal plasma or serum. In particular, the present invention relates to methods which rely on the analysis of polymorphic alleles of a population to determine an allele which is possessed by the fetus but absent from the mother. Fetal specific alleles identified using the methods of the invention can be used to quantify fetal DNA from maternal plasma or serum. In addition, antigens encoded by alleles identified using the methods of the invention can be targeted in methods of isolating or detecting fetal cells.