Background: Adolescents and young adults (AYAs) are a very unique subset of our population journeying through a dynamic stage of their lives. This age group often remains understudied as a separate entity because they are commonly lumped into either pediatric or adult subgroups. Methods: Here we review acute and chronic issues surrounding hematopoietic stem cell transplantation (HSCT) with a focus on the AYA age group. Results: HSCT is a commonly used treatment modality for patients with certain types of cancers. AYA patients undergoing HSCT present a very unique perspective, circumstances, medical, psychological and social issues requiring a diligent workup, care and follow-up. Conclusion: The medical care of these patients should be approached in a multidisciplinary method involving the patient, caregivers, physicians, psychologists and social workers.