miRNAs are small (∼22 bp) RNAs. They play central roles in many cellular processes. Epstein-Barr virus (EBV) is an important human pathogen that establishes persistent infection in nearly all humans and is associated with several common forms of cancer. To achieve persistent infection, the virus infects B cells and uses a series of discrete transcription programs to drive these B cells to become memory B cells – the site of long term persistent infection. It was the first human virus found to express miRNAs of which there are at least 40. The functions of a few of these miRNAs are known but their expression in latently infected normal and neoplastic tissues in vivo have not been described. Here we have profiled EBV miRNAs in a wide range of infected normal and neoplastic tissue. We demonstrate that there are indeed latency program specific patterns of viral miRNA expression and that these patterns are disrupted in EBV associated tumors implicating EBV miRNAs both in long term persistence and in oncogenesis.