Low bone mineral density (BMD) has been reported in recipients of pediatric hematopoietic cell transplantation (HCT), but it is unclear whether age at HCT has a role. The objective of this cross-sectional study was to determine if patients treated with HCT before the age of 10 years have long-term BMD deficits compared with patients transplanted at an older age and with sibling controls. The study included 151 HCT recipients (87 males), age at study 24.7±8.6 years treated with HCT for hematologic malignancies at age 10.9±6.4 years, and 92 healthy sibling controls (49 males), age at study 22.3±8.0 years. Dual-energy x-ray absorptiometry was performed to measure BMD Z-scores for total body BMD (TBMD), lumbar spine BMD (LBMD) and femoral neck BMD (FNBMD, for subjects 20 years at study visit). Patients <10 years at HCT had significantly lower TBMD and FNBMD Z-scores (by 0.5 and 0.8 s.d., respectively) compared with controls (P=0.003 and P=0.0001, respectively) and patients >18 years at HCT (P=0.04 and P=0.004, respectively) at an average of 14 years after HCT. In conclusion, this study identified young age at transplant as an important risk factor for bone deficits in young adulthood, suggesting that efforts to reduce bone loss should focus on this patient population.Bone Marrow Transplantation advance online publication, 14 October 2013; doi:10.1038/bmt.2013.156.