Successful detection of circulating nucleic acids has opened up new possibilities in cancer testing and prenatal diagnosis. Circulating DNA markers are useful in cancer detection, prognostication and monitoring. Cancer-associated molecular changes which can be detected include gene mutations, chromosomal rearrangements, microsatellite alterations, viral sequences, and, to be discussed in more detailed, gene promoter hypermethylation. Methylation analysis is commonly performed by DNA digestion with methylation-sensitive restriction endonucleases followed by polymerase chain reaction (PCR), or bisulfite modification followed by methylation-specific PCR (MSP). The detection of fetal DNA in maternal plasma has opened up new possibilities for noninvasive prenatal diagnosis. However, circulating fetal DNA detection has been based on exploiting gender and polymorphic differences between the fetus and mother. The recent discovery of epigenetic differences between the maternal and the fetal DNA detectable in maternal plasma has launched a hunt for fetal-derived epigenetic markers in maternal plasma. It is hoped that this type of universally applicable markers would be made available in a clinical diagnostic setting in the near future.