Despite its high effectiveness, hematopoietic stem cell transplantation (HSCT) can sometimes be associated with multiple peri-transplant complications requiring urgent intervention. Life-threatening complications in the transplantation unit affect non-relapse mortality. This article sets out a practical approach to the essential peri-transplant clinical conditions, divided into infectious complications and complications related to immune response and endothelial damage. An early diagnosis of life-threatening conditions, and prompt implementation of the best therapy, can save patients' lives. This is especially the case regarding infectious complications in neutropenic patients and in the advanced stages of immunological complications such as graft-versus-host disease, veno-occlusive disease, graft failure, diffuse alveolar hemorrhage, and thrombotic microangiopathy associated with HSCT. These emergencies are discussed below, along with their risk factors and a summary of the management of patients in the early post-transplant period.