Due to their homing properties, extranodal marginal zone B-cell lymphoma (MZBL) of mucosa-associated lymphoid tissue (MALT) type remain localized for long periods of time, and therefore have an excellent prognosis. However, if generalization and/or transformation into a diffuse large-cell lymphoma occurs, the prognosis deteriorates and no established treatment concepts are yet available. We report about a 57-year-old female patient with relapsed transformed stage-IV extranodal MZBL of MALT type of the entire gastrointestinal tract who was successfully treated using salvage chemotherapy followed by BEAM conditioning [BCNU 1,3-bis-2-(chloroethyl-1-nitrosourea), etoposide, cytosine arabinoside, and melphalan] and autologous peripheral stem cell transplantation. Follow-up revealed a sustained complete remission for 22 months.