Mucosa-associated lymphoid tissue (MALT) lymphoma with t(11;18)(q21;q21), resulting in an API2-MALT1 fusion transcript, is reported to rarely transform into aggressive lymphoma. Here, we report the clinical course of a patient who experienced histologic transformation after 20 years' disease history of t(11;18)-positive MALT lymphoma. The patient suddenly developed a large intrapelvic mass and ascites with a rapid increase in lactate dehydrogenase. Cytology of the ascites detected large abnormal cells, and flow cytometric analysis revealed that the cells were positive for cytoplasmic CD3, CD4, and CD38, and partially positive for CD7, but negative for CD19 and CD20. Antigen receptor gene rearrangement analysis and in situ hybridization of the immunoglobulin light chains confirmed that the tumor cells were of B-cell lineage. Chromosomal analysis showed complex karyotypes with intraclonal variation, and in addition to t(11;18), t(8;14) and heterozygous loss of the TP53 were demonstrated. Although histological and phenotypic features were significantly altered from the original MALT lymphoma, the presence of t(11;18) led us to the diagnosis of histologic transformation of MALT lymphoma. Although transformation of t(11;18)-positive MALT lymphoma into aggressive lymphoma is extremely rare, it may occur, probably with additional genetic abnormalities such as cMYC rearrangement and/or the loss of TP53.