: Breast cancer (BC) is the most common source of new cancer diagnoses among women and the second leading cause of cancer-related deaths in this group. The role of viral factors in the etiology, heterogeneity, and pathogenesis of this disease and its subtypes has not been incontrovertibly determined. Thus, in this study we began to address this problem by testing the hypothesis that the oncogenic Epstein-Barr virus (EBV) plays a role in this process. The approach involved determining the differential expression and predicted role of EBV gene sequences present in various subtypes of breast tumors as compared to those in control normal tissues. : We utilized existing deep sequencing RNA-seq datasets derived from seventeen breast tumors and three control normal breast tissue samples to investigate the differential expression of EBV gene sequences. : We report three-fold higher levels of normalized total EBV-expressed sequences in tumors as compared to in control breast tissue. We also demonstrate differential expression of EBV gene transcript sequences in four categories of 26 known genes in breast cancer tumors as compared to that in normal breast tissue controls. Tumor-specific expression of EBV gene transcript sequences localized to seventeen genes; of these, tumor-specific EBV gene transcript-expressed sequences localizing to nine genes were strongly differentially expressed in a breast cancer subtype-specific manner. Furthermore, in a proof-of-concept investigation, we report, for the first time, that functional analysis of the differentially expressed integrated EBV transcript sequences demonstrate the capacity of these sequences to generate novel EBV miRNAs. We conclude that these integrated EBV sequences could potentially play a role in the pathogenesis of BC and its most aggressive subtypes. The functional role of these findings is currently under study.