While Epstein Barr virus (EBV) is associated with about 10% of gastric carcinomas worldwide, the role of the virus in the tumorigenesis of EBV-associated gastric carcinoma (EBVaGC) is unclear. Previously, we reported that a gastric cancer cell line, SNU-719, that is naturally infected with EBV closely resembles EBVaGC. Here, we attempted to eliminate the EBV genome from SNU-719 cells to ascertain the influence of EBV in EBVaGC. Southern blotting and fluorescence in situ hybridization (FISH) showed that EBV genomes were maintained as episomes in SNU-719 cells. To remove EBV episomes, SNU-719 cells were first cultured in a hydroxyurea (HU)-containing medium for up to 6 months. Real-time polymerase chain reaction and FISH results revealed no evidence of HU-mediated EBV genome reduction, although cell growth was reduced by acute HU treatment in dose- and time-dependent manners. Two small interfering RNAs against Epstein Barr nuclear antigen 1 (EBNA1) abrogated over 90% of the ectopic EBNA1 expression in HeLa cells, but only 40% of endogenous EBNA1 expression in SNU-719 cells. Together, our data suggest that maintenance of latent EBV infection is essential for the viability of EBVaGC cells, avoiding elimination of EBV episomes from the cells.