Eighteen patients (12 men and 6 women) with aplastic anemia and active fungal infections (10 proven/probable; 8 possible) underwent stem cell transplantation using fludarabine combined with cyclophosphamide or total body irradiation. Peripheral blood stem cells (PBSC) were the main graft source and a combination of cyclosporine with either methotrexate or methylprednisolone was used for graft versus host disease prophylaxis. Fourteen patients (77.8%) achieved neutrophil engraftment after a median time of 11 d, while four died of fungal sepsis. Resolution of fungal infection occurred in 60% of patients with proven/probable infections and in 100% with possible fungal infections. At a median follow up of 30 months, 11 patients (61.1%) were alive and well. Fludarabine-based conditioning regimens with PBSC transplantation can be used successfully in patients with aplastic anemia and fungal infections.