Thalassemia and the blood transfusion complications associated with it predispose children to poor bone health. This study was conducted to determine the prevalence of bone-related abnormalities and identify the bone health predictors within this population. One hundred and forty transfusion-dependent beta thalassemic subjects 8-18 years old in Mashhad, Iran, participated in this cross-sectional study. Anthropometric measures, dietary intake, bone-related biomarkers and bone densitometry, were assessed. The incidence of underweight and short stature was 33.6 and 41.4 %, respectively, which were indicators of malnutrition among thalassemic subjects in this study. Low bone density was detected in the lumbar spine and femoral region in 82 and 52 % of subjects, respectively. Hypocalcemia and hypophosphatemia were seen in 22 and 18.2 %, whilst vitamin D deficiency was present in more than 85 % of thalassemic children and adolescents. The relationships between weight, height and other anthropometric indices, serum calcium and bone markers, intake of macronutrients, zinc and vitamin E with bone mineral density (BMD) and bone mineral content (BMC) in the lumbar spine and femoral area were positively related, indicating that better nutritional status were associated with higher BMD and BMC values. Puberty, gender and serum osteocalcin were negative predictors for BMD and BMC values, whereas age, weight and height were the positive predictors. High incidence of low bone density and deficit in other aspects of bone health among thalassemia patients makes routine bone health assessment necessary for this vulnerable group. Considering influencing factors, dietary counseling and preventive supplementation therapy for this high risk group of children and adolescents may be necessary, although this should be assessed by intervention studies.