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The pathogenesis of bladder marginal zone/mucosa-associated lymphoid tissue (MALT) lymphoma, which is the most common type of primary bladder lymphoma, has not been clarified. There are no reports that described histological and molecular time course of MALT lymphoma occurring in the bladder and the importance of the score on the Pelvic Pain and Urgency/Frequency (PUF) patient symptom scale during and after radiation therapy (RT). We present a case of MALT lymphoma with long-term comparative genetic analysis. A 77-year-old Japanese woma