The long-term quality of life of patients after hematopoietic stem cell transplantation (HSCT) represents a multidisciplinary problem. HSCT can induce damage of various organs and tissues-from minimal potentially progressive subclinical changes to life-threatening conditions. Endocrine complications are among the most common late effects observed in survivors after HSCT. The relative risk of these complications is likely to be influenced by the underlying disease, type of therapy, and age at HSCT. Understanding the pathogenetic mechanisms of late complications that can occur after HSCT provides a basis for optimal surveillance and early intervention. Further research is needed for improved risk stratification of patients who are at low and high risk of developing late toxicity. Through collaboration between pathophysiologists, clinicians, and patient associations we can enhance the implementation of prospective studies and set forth effective preventive programs for survivors after HSCT.