Lymphomatoid granulomatosis (LG) is a rare lymphoproliferative disorder. There is no standard therapy for refractory patient. Here we present the case of a patient with LG of the lung and the brain who was refractory to polychemotherapy. An autologous hematopoietic stem cell transplantation was done and the patient achieved a complete remission. This represents the first case of high-dose chemotherapy with hematopoietic stem cell support in this disease.