For many years cancer research has focused on genetic defects, but during the last decade epigenetic deregulation has been increasingly recognized as a hallmark of cancer. The advent of genome-scale analysis techniques, including the recently developed next-generation sequencing, has enabled an invaluable advance in the molecular mechanisms underlying tumor initiation, progression, and expansion. In this review we describe recent advances in the field of cancer epigenomics concerning DNA methylation, histone modifications, and miRNAs. In the near future, this information will be used to generate novel biomarkers of relevance to diagnosis, prognosis, and chemotherapeutic response.