Primary lymphoepitheliomalike carcinomas (LELC) of the esophagus are uncommon, with only 29 previously reported cases in the literature. Primary LELC of the esophagus is associated with Epstein-Barr virus (EBV). We herein report a 52-year-old man who presented with dysphagia and weight loss and was found to have a polypoid mass in the middle esophagus. Pathologic examination showed LELC. EBV infection was demonstrated by immunohistochemical detection of EBNA-1 in neoplastic cells and polymerase chain reaction amplification for EBNA-3C, BamHI-F, and W1/I1 regions but not by in situ hybridization by EBER-1 transcripts. EBV genotyping analysis demonstrated infection by a novel type "i"/XhoI loss recombinant strain. Although it is accepted that polymorphisms at BamHI-W1/I1 region cosegregate with polymorphisms at XhoI restriction site, this novel recombinant EBV has been identified in healthy donors and in nasal NK/T-cell lymphoma. To our knowledge, this is the first report that describes this recombinant type "i"/XhoI loss EBV strain in a primary LELC of the esophagus.