The objective of this study was prospectively to investigate the health-related quality of life (HRQOL) of 80 pediatric recipients of allo-SCT for malignant and non-malignant diseases. The PedsQL 4.0 was used to assess self-reported physical, emotional and social functioning of children X5 years old once, pre-allo-SCT and on days þ 100, þ 180, þ 365 and þ 730. Emotional and social functioning was stable pre-to-post-allo-SCT and comparable to the normative sample (P40.05), and physical functioning was 17 points lower pre-allo-SCT (Pp0.01) with improved scores equivalent to the norms by day þ 730. Lower physical scores were reflected by 50-54% of children reporting difficulties with movement, strength, pain and fatigue. At baseline, children ages 5-7 reported lower social functioning (Po0.05) and patients with non-malignant disease reported better physical functioning (Po0.05). Emotional functioning in ages 8-12 improved over time (Po0.05). More than 50% of the participants were minority and their HRQOL was similar to non-minority participants. Physical functioning significantly improved for recipients of reduced-toxicity conditioning (Pp0.01), significantly worsened for patients with chronic GVHD (cGVHD; Po0.05), and significantly decreased in recipients of matched-unrelated donor transplant who developed cGVHD (Po0.05). Multidisciplinary efforts are necessary to identify and support pediatric patients' physical needs to improve functional outcomes.