Epstein-Barr virus (EBV) is a double stranded DNA virus of the family Herpesviridae. EBV is associated with a variety of lymphomas, and the mechanisms by which it promotes lymphomagenesis have been elucidated; this includes, for example, by translocation/activation of Myc in Burkitt lymphoma. However, the mechanisms by which it induces lymphoid tumors other than Burkitt lymphoma are unclear. Recently, we reported that the genome of EBV present in EBV-associated lymphomas harbors frequent intragenic deletions and that the deletion of a gene essential for virus replication promotes lymphomagenesis in a mouse model. Although intragenic deletions have been detected in other tumor viruses, little is known about the effects and importance of those of EBV, a large DNA virus whose genome encodes more than 70 genes. In this review, we summarize the role of EBV in lymphomagenesis with a focus on the impact of intragenic deletions.