Objective The advanced solid tumor in children is not responsive to regular chemotherapy. This paper aims at studying the feasibility and effect of high dose chemotherapy combined with autologous peripheral stem cell transplantation (APBSCT) in the treatment of high risk advanced solid tumors in children. Methods Thirteen patients, including 7 cases of malignant lymphoma and 6 cases of neuroblastoma, were given APBSCT after receiving complete remission (CR) or partial remission (PC). The median disease duration before transplantation was 10 months. Before transplantation, 12 patients had CR and 1 had PR. Mobilization of stem cells was performed with chemotherapy plus G CSF or GM CSF in 11 and chemotherapy alone in 2 patients. The collecting mean number of MNCs, CD34 + cell and CFU GM was ( 6.85 ± 2.65 )×10 8/kg, ( 15.82 ± 12.93 )×10 6/kg and 17.87 ± 17.94 colons/10 4 cell respectively. The conditioning regimen consisted of cyclophosphamide plus TBI as basic program in 6 patients, melphalan plus etoposide, carboplatin in 5 patients and busulfan plus melphalan in 2 patients. Results The median times of the amount of WBC being more than 0.5 ×10 9/L and 1.0 ×10 9/L and of thrombocytopenia being more than 20×10 9/L were 12, 15 and 19 days respectively. A follow up of 48 months (ranging from 1 month to 144 months) showed that survival and death rates after transplantation were 77% (10/13) and 23% (3/13) respectively. No death due to the transplantation was found. Conclusion APBSCT can significantly improve the prognosis of patients with advanced solid tumors.