Background: More than 20000 patients with beta-thalassemia have been identified in Iran, and as survival improves in major thalassemia, endocrine and bone mineral density complications are emerging as a significant problem. The main objective of this study is to compare bone mineral density (BMD) and some metabolic markers of thalassemic patients with a healthy population.Methods and Participant: A total of 208 thalassemic patients and 235 controls, aged 10-20 years in Tehran-Iran entered the study, and distributed in 22 age-sex matched groups. BMD of lumbar spine and femur were determined by dual-energy X-ray absorptiometry (DXA). Height, weight, pubertal development, calcium intake, serum calcium, phosphate, 25(OH) D, and iPTH of participants were measured. Results: Mean of lumbar BMD in all thalassemic patients were significantly lower than the control subjects. in femoral region, mean of BMD was significantly lower in thalassemics in most of subgroups (13,14,15,16,17,19 and 20 year old males; and 12,14,16 and 19year old females).The amount of calcium intake was significantly lower in thalassemics (P<0.05). There was no significant difference between serum levels of 25 (OH)D in two groups. Mean of serum iPTH was thalassemics(p<0.0005).Conclusions: Bone mineral lower in density disturbance, especially in lumbar region is a common finding in adolescent thalassemic patients. The probable association between bone mineral metabolism and related metabolic markers demands further investigation.