Introduction: Beta-thalassemia major patients frequently have endocrine and metabolic disorders. As Iranian studies are scarce; we studied thalassemia major effects on glucose metabolism, endocrinological, BMD and bone metabolism parameters in Iranian patients in a cross sectional study. Materials and methods: Thirty beta-thalassemia major patients with mean age of 18.2 ± 11 (2-45 y/o) entered the study. Females were 8 cases. Children were 18 cases (less than 20 y/o). Medical history collected and serum levels of ferritin, prolactin, LH, FSH, T4, T3, TSH, IGF-1, testosterone (in males) or estradiol (in females) ACTH, cortisol and Bone-specific alkaline phosphatase and osteocalcin (bone formation markers), NTX (bone resorption marker), Ca, P, Alk ph, PTH and Vit D determined. BMD measured by Hologic Discovery QDR model. Results: Diabetes, impaired fasting glucose (IFG), low IGF1, short stature, subclinical hypothyroidism, hypocortisolism high prolactin level were found in 7%, 10%, 63%, 40%, 10%, 10% and 6.6% of our patients, respectively. Low Vit-D and Z-score ≤ -2 in spinal and femoral regions (neck and total) found in 76%, 43%, 20% and 16% of our patients. Women showed significantly higher FSH (p-value=0.048). Ferritin related only with prolactin and LH (negatively) and positively with Phosphorous (p-values: 0.027, 0.049 and 0.016 respectively). Age related positively to height, weight, BMD of femoral (neck and total) and spinal regions (p-values< 0.001, <0.001, 0.005, 0.013 and <0.001, respectively). T3, total alkaline phosphatase, bone specific alkaline phosphatase, NTX and Z-scores of total femoral and spinal regions related negatively with age (p-values, 0.006, 0.041, 0.008, 0.015 and <0.001, respectively). Mean of ferritin level was significantly higher in diabetic patients (p-values <0.00). Mean age of patients with diabetes, IFG, short stature patients and who had Z-score less than -2 in spinal region were significantly higher than those who were normal (p-values: 0.024 and 0.002 respectively). Conclusion: The main factor related with diabetes, IFG short stature and lower Z-scores of the femur and spine was age. So, we recommend early monitoring of thalassemia patients (in their childhood) for these complications.