Lymphoepithelioma-like carcinoma (LEC) of the colon is very rare. Here we report a case of LEC originating in the rectum that was closely associated with Epstein-Barr virus (EBV) infection. The histologic and immunohistologic features, namely, poorly differentiated adenocarcinoma with lymphoid stroma, showed this tumor to be an LEC. The EBV genome was detected by PCR using DNA obtained from tumor tissue sections. Immunohistochemically, EBV-determined nuclear antigen 2 was detected in the tumor cells, and in situ hybridization using EBV-encoded small RNAs probe showed positive labeling in some tumor cells together with a few stromal lymphoid cells. There are some reports of LEC cases that originated in the colon; however, a relation with EBV was not demonstrated. We report here a case of LEC of the rectum demonstrating a possible relation with EBV.