Eukaryotic genomic information is modulated by a variety ofepigenetic modifications that play both a direct role in establishing transcription profiles, modulation of DNA replication and repair processes and also indirect effects on the aforementioned processes through the organization of DNA architecture within the cell nucleus. Nowadays, the role of epigenetic modifications in regulating tissue-specific expression, genomic imprinting or X-chromosome inactivation is widely recognized. In addition, the key role of epigenetic modifications during cell differentiation and development has been highlighted by the identification of a variety of epigenetic alterations in human disease. Particular attention has been focused on the study of epigenetic alterations in cancer, which is the subject of intense multidisciplinary efforts and has an impact not only in understanding the mechanisms of epigenetic regulation but also in guiding the development ofnovel therapies for cancer treatment. In addition, a number of genetic disorders such as immunodeficiency-centromere instability-facial anomalies (ICF) or Rett syndromes are directly associated with defects in elements of the epigenetic machinery. More recently, epigenetic changes in cardiovascular, neurological and autoimmune disorders as well as in other genetically complex diseases have also started to emerge. All these examples illustrate the widespread association ofepigenetic alterations with disease and highlight the need of characterizing the range and extension of epigenetic changes to understand their contribution to fundamental human biological processes.