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Hematopoietic cell transplantation (HCT) may be detrimental to bone health and vitamin D status in children.We conducted a prospective, multicenter cohort study to identify changes in bone health markers during the first 100 days after allogeneic HCT in 26 children. Bone mineral density (BMD), bone mineral content (BMC), and serum 25-hydroxyvitamin D (25OHD) concentrations were measured at baseline, 30 days, and 100 days after HCT.Mean (SD) BMD and BMC Z-scores (−0.48 ± 1.09 and −0.98 ± 1.26, respectively) were normal at baseline. Repeated-measures analysis revealed significant declines in BMD and BMC Z-scores over the 100 day study period, when adjusted for age, sex, Tanner stage, lean mass, fat mass, resting energy expenditure, total energy intake, insulin sensitivity, serum phosphorus, and inpatient steroid intake. Adjusted mean (SE) 25OHD concentrations declined from 29.2 (3.1) ng/ml at baseline, to 17.7 (1.8) ng/ml at 100 days after HCT. Vitamin D deficiency (25OHD <20 ng/ml) was present in 50% of patients 100 days after HCT.Significant bone loss and vitamin D deficiency occur in children in the first 100 days following allogeneic HCT. Strategies to diminish acute bone loss during HCT in children are needed. Pediatr Blood Cancer 2015;62:687–692. © 2015 Wiley Periodicals, Inc.