For the first time, the development of next-generation sequencing technologies has brought about tools to investigate epigenetic alterations in an unbiased, yet genome-wide approach. The importance of this innovative technology is undeniable since it has already been established that changes in DNA methylation play an important role in cancer initiation and progression. The first methylation maps have already been created, and it is only a matter of time until the complete epigenetic maps of healthy and diseased human genomes are available. In this review, we summarize the use of next-generation sequencing for diverse epigenetic technologies, give an overview of the status quo and outline future perspectives for its application in oncology and basic research.