Despite recent advances in iron chelation therapy, excess iron deposition in pituitary gonadotropic cells remains one of the major problems in thalassemic patients. Hypogonadism, mostly hypogonadotropic hypogonadism, is usually detected during puberty. Early diagnosis and treatment are crucial for normal pubertal development and to reduce the complications of hypogonadism. The risks and benefits of hormonal replacement therapy, especially regarding the thromboembolic event, remain a challenge for providers caring for thalassemic patients.