Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment for patients with a hematologic disease. Although the clinical outcomes after allo-HCT have significantly improved during the last few decades, graft-versus-host disease (GVHD) is still a major cause of post-HCT morbidity and mortality. Systemic glucocorticoids (GC) remain an integral part of treatment in patients with GVHD including both acute and chronic GVHD. Although it is well-known that usage of systemic GC is associated with various side effects, the short- and long-term effects of GCs in the HCT setting are not well-characterized due to limited published data. In order to clarify this issue, we summarize the information on side effects associated with GCs, focusing specifically on the sequelae of these agents in the early post-HCT period. In instances where limited data are available, we included data from other fields such as autoimmune diseases, given the potential parallels between autoimmune conditions and GVHD.