Primary low-grade mucosa-associated lymphoid tissue (MALT) lymphoma of the stomach has a potential to transform to high-grade diffuse large B-cell lymphoma (DLBCL). However, the clonal relation between MALT lymphoma and de novo DLBCL is still controversial. We report here three patients with Helicobacter pylori (H. pylori)-positive gastric MALT lymphoma rapidly progressing to DLBCL at the same site after successful eradication of H. pylori. Although MALT lymphomas in our cases did not possess t(11; 18)(q21;q21), sequence analysis of the rearranged immunoglobulin heavy chain gene showed no clonal relation between preceding MALT lymphoma cells and de novo DLBCL cells at the same site. These findings question the scenario of direct clonal progression of low-grade MALT lymphomas without t(11; 18)(q21;q21) to DLBCL and serve as a reminder of the risk of the progression of DLBCL with a distinct clonality immediately after H. pylori eradication for low-grade MALT lymphoma.