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Outcomes for high-risk neuroblastoma remain poor. Modern treatment protocols utilizing intense induction followed by myeloablative consolidation chemotherapy with autologous stem cell rescue (ASCR) have improved survival rates, but the long-term sequelae, including development of secondary malignant neoplasms (SMN), are just now surfacing.We retrospectively reviewed data from 87 patients with high-risk neuroblastoma who were treated with intensive induction chemotherapy followed by ASCR between January 1991 and July 2011 following one of two institutional protocols: Chicago Pilot 1 (CP1; n = 12) and Chicago Pilot 2 (CP2; n = 75).The 15-year overall survival rate for all 87 patients was 33.9% (95% confidence interval [CI], 23.1–45.0%). The 10- and 15-year cumulative incidence of SMN was 16.5% (95%CI, 7.2–38.0%) and 34.2% (95%CI, 18.6–63.1%), respectively, without evidence of a plateau at 15 years. Six of the 10 patients (n = 2 in CP1 and n = 8 in CP2) who developed SMN had hematologic malignancies including acute myeloid leukemia (AML)/myelodysplastic syndrome (MDS). Solid tumors included thyroid papillary carcinoma, chondrosarcoma, hepatocellular carcinoma, and biliary adenocarcinoma.A significantly higher incidence of SMN, especially hematological malignancies, was observed in this cohort compared to older neuroblastoma studies, potentially due to exposure to epipodophyllotoxins and a high cumulative dose of alkylating agents these patients received. The risk of developing an SMN continued to increase with survival time and did not reach the plateau at 15 years. Although the number of the patients is relatively small, our study emphasizes the need for life-long follow-up of survivors who were treated using modern therapy. Pediatr Blood Cancer 2014; 61:1350–1356. © 2014 Wiley Periodicals, Inc.