Enteropathy-type T-cell lymphoma (ETL) is an intraepithelial T-lymphocyte (T-IEL) tumor. The tumor cells are usually CD3+, CD4-, CD8+, and contain cytotoxic granule associated proteins. We report on a CD3-negative CD56-positive enteropathy-associated lymphoma (ETL). This is the first case report of CD3-negative, CD56-positive, CD94-negative, and CD161-positive ETL. ETL cells originate from intraepithelial T-lymphocytes of the intestine. CD3-negative intraepithelial lymphocytes are known as natural killer (NK)-IELs. The phenotype of NK-IELs is also CD3-negative, CD56-positive, CD94-negative, and CD161-positive, while most normal NK cells express CD56 and CD94. CD3-negative lymphoma cells in this report also expressed CD56 and CD161, but not CD94. Because Southern blotting analysis showed a rearrangement of T-cell receptor (TCR) Cbeta in this case, the tumor is classified as an ETL. Based on the findings, NK-IELs may originate from T-cells, not NK-cells.