As autologous stem cell transplantation has a better survival rate than conventional chemotherapy, some prognostic factors are effective on survival and event in children with high risk NBL after autologous stem cell transplantation. This is a retrospective study. We aim to evaluate the effect of clinical and treatment features of 26 patients [Newly diagnosed / Relapsed 15 (57.7%) / 11 (42.3%)] with high-risk neuroblastoma (NBL) undergone to autologous stem cell transplantation with Busulphan-Melphalan or CarboplatinEtoposid- Melphalan. They were included in the study between 1998 and 2015. We aim to evaluate the effect of clinical and treatment features of them on outcome of autologous stem cell transplantation. EFS and OS were 21.4% and 61.8% at 3-year, but they were 14.2% and 53% at 5-year in patients with high-risk NBL. Post-transplant PFS and OS in patients with high risk were 31% and 51.7 at 3-year. Accordingly conditioning regimen, post-transplant PFS and OS rates were 51.9% and 25% in Bu-Mel, 45.5% and 44% in CEM group at 3-year (OS; p= 0.42 and PFS; p= 0.10). Unfavorable histology (p= 0.07, HR= 3.2, CI: 0.9-11.2) was effective factor on EFS, although it was not statistically significant. Remission status (without CR) at auto-SCT was effective factor on both PFS (p= 0.01, HR= 4.6, CI: 1.4-14.9) and OS (p= 0.04, HR= 5.1, CI: 1.1-24.2). Too deep and long-lasting hematologic toxicity was our experience in MIBG treatment before CEM conditioning regimen compared to Bu-Mel. Any conditioning transplant regimen is not superior to each other exactly. The major factors affecting the prognosis of children with neuroblastoma seem tumor load and unfavorable histology. Before autologous stem cell transplantation, complete remission status is essential for progression free and overall survival.