INTRODUCTION: Allogeneic hematopoietic cell transplantation (alloHCT) is the standard of care for many diseases. However, survivors often present with serious complications resulting from acute and chronic toxicities and it is crucial to increase consciousness from treating physicians. AREAS COVERED: We performed a comprehensive review of the literature and critically examined recent available data, mostly using the PubMed and Medline search engines for original articles published over the last decade. Better understanding of many alloHCT-related disorders has shown that endothelial injury and vascular damage plays a critical role. EXPERT OPINION: The most widely studied endothelial injury syndromes (EIS) are veno-occlusive disease/sinusoidal obstruction syndrome (SOS/VOD), graft-versus-host-disease (GVHD), and transplant-associated thrombotic microangiopathy (TA-TMA). TA-TMA, frequently underdiagnosed, needs to be clarified using certain criteria and, as a life-threatening condition, requires immediate and intensive treatment. The first-in-class complement inhibitor eculizumab has significantly improved outcomes in both the pediatric and adult population. Cardiovascular (CV) events are the second major cause of morbidity and mortality of alloHCT survivors, after GVHD. Long-term monitoring and management of CV risk is expected to also incorporate patient stratification with CV risk prediction models, early markers of vascular dysfunction or procoagulant activity, subclinical target organ damage, arterial stiffness, and subclinical atherosclerosis.