Despite remission rates of approximately 85% for children diagnosed with acute myeloid leukemia (AML), greater than 40% will die from relapsed disease. Patients with poor-risk molecular/cytogenetics and/or inadequate response to upfront therapy are typically considered high-risk (HR) and historically have poor outcomes with chemotherapy alone. We investigated whether allogeneic hematopoietic cell transplantation (allo-HCT) with best available donor in first remission (CR1) would abrogate the poor outcomes associated with HR AML in chemotherapy treated children and young adults. We reviewed the outcomes of 50 consecutive children and young adults (ages 0–30 years) with AML who received a myeloablative allo-HCT between 2001 and 2010. Thirty-six patients (72%) were HR, defined as having FLT3-ITD mutations, 11q23 MLL rearrangements, chromosome 5 or 7 abnormalities, induction failure and/or having persistent disease. The majority of patients received cyclophosphamide and total body irradiation conditioning and graft-versus-host-disease (GVHD) prophylaxis was cyclosporine based. Transplant outcomes for HR patients were compared to standard-risk patients with no significant differences observed in overall survival (72% vs. 78%, p=0.72), leukemia-free survival (69% vs. 79%, p=0.62), relapse (11% vs. 7%, p=0.71) or TRM (17% vs. 14%, p=0.89). Children and young adults with HR-AML have comparable outcomes to standard-risk patients following allo-HCT in CR1.