It has been several years since the presence of fetal DNA in maternal plasma was first discovered. Numerous potential applications have been reported to date. However, the study of maternal plasma for the prenatal diagnosis of fetal genetic traits has largely centered on paternally inherited autosomal dominant traits. Recently, a number of approaches have been developed that allow the prenatal assessment of autosomal recessive conditions through fetal DNA analysis in maternal plasma. On the other hand, aberrations in fetal DNA concentrations in maternal plasma have been reported in a number of pregnancy-associated conditions. Recent studies have begun to address the possible underlying mechanisms causing such quantitative aberrations. Current studies on circulating fetal DNA have focused on the detection of the paternally inherited fetal-specific alleles in maternal plasma. However, it has been demonstrated that the development of fetal epigenetic markers has great potential to expand the field.