Low grade B cell mucosa associated lymphoid tissue (MALT) lymphoma of the stomach is usually an indolent tumour that remains localised for a long time before dissemination occurs. MALT appears in the stomach in response to infection by Helicobacter pylori, which is present in 80-90% of cases. The pathogenesis of the evolution from chronic gastritis to malignant lymphoma has not yet been fully explained and the exact role of H pylori in the pathogenesis and progression of gastric lymphoma remains unclear. This report describes the case of a 72 year old woman with a low grade B cell MALT lymphoma localised in the gastric fundus, who refused to be treated for eradication of H pylori. The histological diagnosis of B cell MALT lymphoma was supported by both immunohistochemical and molecular genetic analysis. After 11 years of follow up, this MALT lymphoma remained indolent, without local progression or blastic transformation, and the H pylori infection was still persistent, even though the density of bacteria had decreased drastically. Interestingly, two different clonal immunoglobulin (Ig) gene rearrangements were found in two series of biopsies performed with an interval of 11 years. This case report supports the following notions: (1) H pylori associated gastritis is a risk factor for gastric MALT lymphoma, but might not be sufficient by itself for the progression of the disease, and (2) in the evolution of MALT lymphomas, different cell clones characterised by different Ig rearrangements may emerge.