Since the discovery of cell-free fetal DNA in the circulation of pregnant women fetal-specific DNA biomarkers for non-invasive prenatal diagnosis of fetal aneuploidy have been sought. A model system assessing the DNA methylation of placental DNA and adult peripheral leukocyte DNA has been developed previously to represent fetal and maternal plasma DNA. To use DNA methylation to detect specific DNA molecules it is desirable that cellfree plasma DNA maintains the methylation profile of its tissue source. Using the imprinted gene GNAS1, a test has been developed to assess, for the first time the relative abundance of methylated and unmethylated DNA circulating in plasma. Methylated and unmethylated DNA sequences were found in equal abundance. If this finding is applicable to all plasma DNA sequences, we conclude that the steadystate concentration of DNA in methylated and unmethylated form is a reliable indicator of its input into the circulation. We have also investigated whether the abundances of different single copy gene sequences in cell-free plasma DNA are equal. Using real-time PCR, the relative abundances of six unique genomic DNA sequences in plasma were assessed. We find that plasma DNA from different sequences is not present in equal abundance in normal healthy individuals. The relative abundance of sequences tested differed by as much as 12.3 fold. We present a panel of novel candidate epigenetic biomarkers which have been identified using the model system. Of 366 DNA regions tested 3% were found to be differential. Further characterisation of these candidate epigenetic biomarkers has revealed limitations of the model system. In view of these results, future epigenetic biomarker development should be achieved by a direct assessment of first trimester plasma DNA.