The Epstein-Barr virus (EBV) genetic map underpins all our understanding of the virus biology and its role in disease. EBV was the first large DNA virus to be fully sequenced and this has been followed by many years of detailed mapping of viral genes and other genetic elements. The genetic map of EBV is based on the reference NC_007605 virus genome but now more than 1,000 EBV genomes have been sequenced. Some sequence variations that may be functionally significant either for the biological properties of EBV or its detection by diagnostic procedures are summarised here but are also considered in detail in other chapters in this book.