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This cross‐sectional study evaluated the overall bone health and the prevalence of vertebral complications after stem cell transplantation (SCT) in prepubertal children and adolescents.A total of 44 children and adolescents (median age, 10 years) were evaluated at a median of 3.8 years after SCT for areal bone mineral density (aBMD) with dual‐energy X‐ray absoptiometry and for vertebral fractures with instant vertebral assessment. Pretransplant and posttransplant medications and nutritional parameters were recorded, and plasma levels of vitamin D, calcium, phosphate, and parathormone were measured.Of the 44 patients, 16 (36%) had a BMD Z‐score of <−1.0. The patients with low BMD did not differ from the others with regard to their clinical or biochemical characteristics. Prepubertal patients had better BMD Z‐scores at all sites compared with pubertal or postpubertal subjects. This was evident especially at the hip, in which the median aBMD Z‐score in prepubertal patients (−0.2; range, −0.5 to +1.7) was found to be significantly higher than in pubertal (−1.1; range, −1.5 to +0.4) and postpubertal (−1.1; range, −2.6 to +0.5) patients (P = .03). Five patients (11%) had a history of peripheral fractures. Nine patients (20%) had vertebral compression fractures, which were asymptomatic in 7 patients.Approximately one‐third of patients who had undergone allogeneic SCT in childhood were found to have a reduced BMD before reaching adulthood. This was due in part to inadequate BMD gain during the pubertal years. The high prevalence of asymptomatic vertebral compression fractures calls for the systematic assessment of spinal health during the posttransplantation follow‐up. Cancer 2007. © 2007 American Cancer Society. [ABSTRACT FROM AUTHOR]