Objective To investigate if low dose total body irradiation (TBI, 6.0- 9.0 Gy) combined with intensified chemotherapy followed by autologous peripheral blood stem cell transplantation results in better survival in children with refractory leukemia or solid tumors. Methods Twenty-one children with malignant tumors were included in this study. There were 14 males and 7 females aged 3.5- 12 years. Underlying disease included high-risk acute lymphoblastic leukemia (ALL, CR1 in 3 children and CR2 in 5 children), acute myeloblastic leukemia (AML, 9 children), non Hodgkin' s lymphoma stage Ⅳ (2 children), and neuroblastoma stage Ⅳ (2 children). The peripheral hematopoietic stem cells were collected six to eleven months after complete response, mobilized with high dose chemotherapy alone or combined with GM-CSF or G-CSF. The conditioning regimen consisted of chemotherapy with two to three combinations of the following drugs: cyclophosphamide, arabinosylcytosine, McNU, etopside, and Idarubicin on the basis of TBI (6.0-9.0Gy). A mean of (1.8 ± 0.5) × 108/kg autologous mononuclear cells were transplanted. The patients were followed up after transplantation. Results Severe bone marrow suppression occurred in all patients around day + 7. Peripheral white blood cell count decreased to 0 in all patients at day + 4.8 ± 2.9, and platelet count decreased to less than 20× 109/L at day + 9.0 ± 2.6. Successful engraftment was achieved in 21 patients, but four died of infection at day + 17, + 20, + 31 and + 67, respectively. Recovery of white blood cell (WBC) to 10 × 109/L, absolute neutrophil count to 0.5 × 109/L, platelet count to 20 × 109/L occurred on 21 ± 12, 26± 13, and 27 ± 10 days, respectively. During the follow up period, three patients relapsed at + 5 months, + 1.5 years, and + 2 years 10 months, respectively. One patient died of intracranial hemorrhage at +8 months. Thirteen patients had event-free survival for 2 - 12 years, with a mean of 6.7±3.4 years. Conclusion Our preliminary data suggest that myeloablative therapy with low dose TBI (6.0 - 9.0 Gy) combined with intensified chemotherapy followed by autologous paripheral blood stem cell transplantation might be associated with favorable results in children with refractory leukemia or solid tumors.