Primary gastric lymphoma usually originates from B cells of mucosa-associated lymphoid tissue (MALT) infected with Helicobacter pylori. When T-cell lymphomas develop in the stomach, they usually occur in association with infection by human T-lymphotropic virus type 1 and gastric involvement of adult T-cell leukemia. Reported herein is a unique and informative case of gastric peripheral T-cell lymphoma with a cytotoxic phenotype that histologically mimicked, and had to be carefully distinguished from, MALT-type B-cell lymphoma. The patient, a 73-year-old woman, underwent a gastric endoscopy examination, and the histological findings suggested MALT-type gastric lymphoma. Analysis of the immunoglobulin heavy chain (IgH) gene and T cell receptor γ (TCRγ) gene revealed monoclonal rearrangement of the TCRγ gene. The tumor cells exhibited mild atypia and immunoreactivity with anti-CD3, anti-CD8, anti-T-cell intracellular antigen-1, antigranzyme B and antiperforin antibodies, but not with anti-CD20, anti-CD10, and anti-CD79a antibodies. The case was finally diagnosed as gastric T-cell lymphoma with cytotoxic phenotype, and this was confirmed after surgical resection. In cases such as this, small biopsy specimens from the stomach should be examined carefully for low grade B-cell-type malignant lymphoma (MALT lymphoma), because sometimes the proliferating B cells can hide the truly malignant T cells, and rearrangement analysis is useful for diagnosing T-cell malignancy.