To clarify the origin of tumor cells and the possible role of antigen in the pathogenesis of mucosa-associated lymphoid tissue (MALT) lymphoma, we analyzed the third complementarity determining region of IgH gene in nine primary gastric B-cell lymphomas by PCR. The presence of vacA gene of Helicobacter pylori was also determined. These cases were diagnosed histopathologically as three low (extranodal marginal zone B-cell lymphoma)- and three high-grade MALT lymphomas and three diffuse large-cell lymphomas without evidence of MALT lymphoma. All cases showed a monoclonally rearranged JH band. A single dominant clone was detected by sequencing the IgH CDR3 regions in eight cases. In the remaining cases. In the remaining case, two major sequences were identified. Complementarity-determining region 3 (CDR3) sequences in lymphoma cell clones of seven cases showed 61% to 81% homology with autoantibody-associated lymphocyte clones including rheumatoid factor. The N-D-N region in the low-grade MALT lymphoma group was significantly longer than in the high-grade lymphoma groups. Although vacA gene of H. pylori was detected in five of nine cases, all lymphoma cell clones showed no association with foreign antigen. These results indicate that autoantigen may be responsible for the clonal selection of lymphoma cells, and thus autoimmunity may play a role in the pathogenesis of primary gastric B-cell lymphomas.