The authors describe a patient with gastric lymphoepithelioma-like carcinoma (LELC) and jejunal low grade B-cell lymphoma of mucosa-associated lymphoid tissue (MALT) with histologic transformation to large cell lymphoma. In situ hybridization studies for Epstein-Barr virus (EBV) demonstrated abundant EBV RNA (EBER) within the neoplastic cells of the gastric LELC and the jejunal large cell lymphoma. The low grade MALT lymphoma was EBER negative. Polymerase chain reaction (PCR) studies confirmed the in situ hybridization results, and demonstrated a 30 base pair deletion in the 3' end of the latent membrane protein gene in both the gastric LELC and the jejunal large cell lymphoma. These results suggest that the same viral strain infected both the stomach and jejunal tumors. In addition, the finding of EBV in the large cell lymphoma, but not the low grade component suggests that EBV may have played a role in large cell transformation.