A 56-year-old man was admitted for treatment of non-Hodgkin's lymphoma (NHL). He had undergone a partial small bowel and colon resection and had ileostomy due to bowel perforation induced by chemotherapy. After the operation, his disease status was in partial remission (PR), and reduced-intensity allogeneic stem cell transplantation (RIST) was therefore performed for further improvement of disease status. The conditioning regimen consisted of fludarabine and busulfan. Graft-versus-host disease (GVHD) prophylaxis was performed using cyclosporin and short-term methotrexate. The occurrence of serious infection during the period of neutropenia was prevented by the administration of amphotericin B, fluconazole and acyclovir. This case report provides important information on the appropriate strategy for treating patients who have ileostomy.