A patient with primary Sjögren's syndrome developed massive gland enlargement and was diagnosed a MALT-type lymphoma stage IIA. After initial radiotherapy the patient relapsed with high grade immunoblastic lymphoma. Chemotherapy led to remission of the lymphoma and improvement of the autoimmune disease. A peripheral blood stem cell harvest was performed. However, subsequent to standard chemotherapy the patient experienced an exacerbation of arthralgia and vasculitis while his lymphoma remained in partial remission. With additional chemotherapy and steroid treatment complete remission of the lymphoma and autoimmune disease was achieved and high-dose chemotherapy followed by PBPCT with an unmanipulated graft was performed. Engraftment was prompt with no signs of active autoimmune disease after the transplantation. Two months later, signs of autoimmune disease slowly recurred. Steroid treatment improved this, but the patient remained steroid-dependent and later died from therapy-resistant Pneumocystis carinii pneumonia while the lymphoma remained in complete remission. In this patient with systemic Sjögren's disease, PBPCT completely controlled the aggressive lymphoma but was not permanently effective for the autoimmune disease.