Cell free DNA (cfDNA) is released from all tissues into the circulation and thus provides promising opportunities for clinical diagnostics. While non-invasive prenatal testing (NIPT), screening for fetal aneuploidies, is probably the best known cfDNA-based method, the use of cfDNA offers a vast potential for various clinical questions. For example, also in the prenatal context, it is possible to detect pathogenic SNVs associated with hereditary diseases in cffDNA using highly sensitive sequencing technologies. Furthermore, in cancer patients, cfDNA analysis enables the identification of circulating tumor DNA (ctDNA), to support treatment decisions and even the detection of residual disease post-surgery or monitoring of response or resistance to treatment. In addition, detection of variants exclusive to certain tissues, such as in mosaic diseases or transplanted organs, can be used to identify the molecular cause of a particular phenotype, such as asymmetric overgrowth syndromes, or to predict organ rejection by identifying increasing amounts of donor derived cfDNA (dd-cfDNA).