The outcome of patients with advanced stage rhabdomyosarcoma is extremely poor, with a disease-free survival of less than 20% at 3 years. Autologous bone marrow transplantation for patients with Clinical Group IV rhabdomyosarcoma may be an effective therapy. The bone marrow involvement diagnosed by light microscopy is 29% for patients with advanced disease. The present study was performed to test the ability of 4-hydroperoxycyclophosphamide (4-HC) to eliminate clonogenic rhabdomyosarcoma cells. Four different human rhabdomyosarcoma cell lines were treated in vitro with 4-HC at a concentration of 100 micrograms/ml. Limiting dilution analysis was performed to detect surviving clonogenic tumor cells. Treatment with 4-HC resulted in 1.7-5.7 log of elimination of clonogenic tumor cells in all four cell lines. Exactly the same log tumor cell kill was obtained after mixing normal human bone marrow mononuclear cells with rhabdomyosarcoma cells. Treatment with 4-HC may be an effective method of eliminating clonogenic rhabdomyosarcoma cells ex vivo.